From 05224b47d2bcdb5ce944430726ead4ce1c55c41d Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Thu, 11 Apr 2019 12:22:45 +0100 Subject: [PATCH 01/14] Created 'derivatives' folder with processed MPM output --- .../sub-01/{fmap => derivatives}/sub-01_B0map.json | 0 .../sub-01/{fmap => derivatives}/sub-01_B1map.json | 0 .../sub-01/{anat => derivatives}/sub-01_MTmap.json | 0 .../{anat => derivatives}/sub-01_MTmap.nii.gz | Bin .../sub-01/{anat => derivatives}/sub-01_PDmap.json | 0 .../{anat => derivatives}/sub-01_PDmap.nii.gz | Bin .../sub-01/{anat => derivatives}/sub-01_R1map.json | 0 .../{anat => derivatives}/sub-01_R1map.nii.gz | Bin .../{anat => derivatives}/sub-01_R2starmap.json | 0 .../{anat => derivatives}/sub-01_R2starmap.nii.gz | Bin 10 files changed, 0 insertions(+), 0 deletions(-) rename examples/ds-04/sub-01/{fmap => derivatives}/sub-01_B0map.json (100%) rename examples/ds-04/sub-01/{fmap => derivatives}/sub-01_B1map.json (100%) rename examples/ds-04/sub-01/{anat => derivatives}/sub-01_MTmap.json (100%) rename examples/ds-04/sub-01/{anat => derivatives}/sub-01_MTmap.nii.gz (100%) rename examples/ds-04/sub-01/{anat => derivatives}/sub-01_PDmap.json (100%) rename examples/ds-04/sub-01/{anat => derivatives}/sub-01_PDmap.nii.gz (100%) rename examples/ds-04/sub-01/{anat => derivatives}/sub-01_R1map.json (100%) rename examples/ds-04/sub-01/{anat => derivatives}/sub-01_R1map.nii.gz (100%) rename examples/ds-04/sub-01/{anat => derivatives}/sub-01_R2starmap.json (100%) rename examples/ds-04/sub-01/{anat => derivatives}/sub-01_R2starmap.nii.gz (100%) diff --git a/examples/ds-04/sub-01/fmap/sub-01_B0map.json b/examples/ds-04/sub-01/derivatives/sub-01_B0map.json similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_B0map.json rename to examples/ds-04/sub-01/derivatives/sub-01_B0map.json diff --git a/examples/ds-04/sub-01/fmap/sub-01_B1map.json b/examples/ds-04/sub-01/derivatives/sub-01_B1map.json similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_B1map.json rename to examples/ds-04/sub-01/derivatives/sub-01_B1map.json diff --git a/examples/ds-04/sub-01/anat/sub-01_MTmap.json b/examples/ds-04/sub-01/derivatives/sub-01_MTmap.json similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_MTmap.json rename to examples/ds-04/sub-01/derivatives/sub-01_MTmap.json diff --git a/examples/ds-04/sub-01/anat/sub-01_MTmap.nii.gz b/examples/ds-04/sub-01/derivatives/sub-01_MTmap.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_MTmap.nii.gz rename to examples/ds-04/sub-01/derivatives/sub-01_MTmap.nii.gz diff --git a/examples/ds-04/sub-01/anat/sub-01_PDmap.json b/examples/ds-04/sub-01/derivatives/sub-01_PDmap.json similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_PDmap.json rename to examples/ds-04/sub-01/derivatives/sub-01_PDmap.json diff --git a/examples/ds-04/sub-01/anat/sub-01_PDmap.nii.gz b/examples/ds-04/sub-01/derivatives/sub-01_PDmap.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_PDmap.nii.gz rename to examples/ds-04/sub-01/derivatives/sub-01_PDmap.nii.gz diff --git a/examples/ds-04/sub-01/anat/sub-01_R1map.json b/examples/ds-04/sub-01/derivatives/sub-01_R1map.json similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_R1map.json rename to examples/ds-04/sub-01/derivatives/sub-01_R1map.json diff --git a/examples/ds-04/sub-01/anat/sub-01_R1map.nii.gz b/examples/ds-04/sub-01/derivatives/sub-01_R1map.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_R1map.nii.gz rename to examples/ds-04/sub-01/derivatives/sub-01_R1map.nii.gz diff --git a/examples/ds-04/sub-01/anat/sub-01_R2starmap.json b/examples/ds-04/sub-01/derivatives/sub-01_R2starmap.json similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_R2starmap.json rename to examples/ds-04/sub-01/derivatives/sub-01_R2starmap.json diff --git a/examples/ds-04/sub-01/anat/sub-01_R2starmap.nii.gz b/examples/ds-04/sub-01/derivatives/sub-01_R2starmap.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_R2starmap.nii.gz rename to examples/ds-04/sub-01/derivatives/sub-01_R2starmap.nii.gz From c0fe1edffc7514bc15a46a401a306cdfe9797de3 Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Thu, 11 Apr 2019 15:09:11 +0100 Subject: [PATCH 02/14] Restructured all 4 examples to have 'derivatives' and 'sourcedata' master folders Fixed small inconsistency in ds-01 (missing T2starmap.nii.gz file) Changed 'MTmap' to 'MTsat' in ds-04 --- .../{ => derivatives}/sub-01/anat/sub-01_QSM.json | 0 .../{ => derivatives}/sub-01/anat/sub-01_QSM.nii.gz | 0 .../sub-01/anat/sub-01_T2starmap.json | 0 .../sub-01/anat/sub-01_T2starmap.nii.gz | 0 .../{ => sourcedata}/sub-01/anat/sub-01_FLASH.json | 0 .../sub-01/anat/sub-01_echo-1_FLASH.json | 0 .../sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-1_part-phase_FLASH.nii.gz | 0 .../sub-01/anat/sub-01_echo-2_FLASH.json | 0 .../sub-01/anat/sub-01_echo-2_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-2_part-phase_FLASH.nii.gz | 0 .../sub-01/anat/sub-01_echo-3_FLASH.json | 0 .../sub-01/anat/sub-01_echo-3_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-3_part-phase_FLASH.nii.gz | 0 .../{ => derivatives}/sub-01/anat/sub-01_T1map.json | 0 .../sub-01/anat/sub-01_T1map.nii.gz | 0 .../sub-01/anat/sub-01_MP2RAGE.json | 0 .../{ => sourcedata}/sub-01/anat/sub-01_T1w.json | 0 .../{ => sourcedata}/sub-01/anat/sub-01_T1w.nii.gz | 0 .../sub-01/anat/sub-01_inv-1_MP2RAGE.json | 0 .../anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz | 0 .../anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz | 0 .../sub-01/anat/sub-01_inv-2_MP2RAGE.json | 0 .../anat/sub-01_inv-2_part-mag_MP2RAGE.nii.gz | 0 .../anat/sub-01_inv-2_part-phase_MP2RAGE.nii.gz | 0 .../{ => derivatives}/sub-01/anat/sub-01_T1map.json | 0 .../sub-01/anat/sub-01_T1map.nii.gz | 0 .../sub-01/anat/sub-01_T2starmap.json | 0 .../sub-01/anat/sub-01_T2starmap.nii.gz} | 0 .../sub-01/anat/json.tool} | 0 .../sub-01/anat/sub-01_MP2RAGE.json | 0 .../{ => sourcedata}/sub-01/anat/sub-01_T1w.json | 0 .../sub-01/anat/sub-01_T1w.nii.gz} | 0 .../sub-01/anat/sub-01_inv-1_MP2RAGE.json | 0 .../anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz} | 0 .../anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz} | 0 .../sub-01/anat/sub-01_inv-2_MP2RAGE.json | 0 .../sub-01/anat/sub-01_inv-2_echo-1_MP2RAGE.json | 0 .../sub-01_inv-2_echo-1_part-mag_MP2RAGE.nii.gz} | 0 .../sub-01_inv-2_echo-1_part-phase_MP2RAGE.nii.gz} | 0 .../sub-01/anat/sub-01_inv-2_echo-2_MP2RAGE.json | 0 .../sub-01_inv-2_echo-2_part-mag_MP2RAGE.nii.gz} | 0 .../sub-01_inv-2_echo-2_part-phase_MP2RAGE.nii.gz} | 0 .../sub-01/anat/sub-01_inv-2_echo-3_MP2RAGE.json | 0 .../sub-01_inv-2_echo-3_part-mag_MP2RAGE.nii.gz} | 0 .../sub-01_inv-2_echo-3_part-phase_MP2RAGE.nii.gz} | 0 .../sub-01/anat/sub-01_inv-2_echo-4_MP2RAGE.json | 0 .../sub-01_inv-2_echo-4_part-mag_MP2RAGE.nii.gz} | 0 .../sub-01_inv-2_echo-4_part-phase_MP2RAGE.nii.gz} | 0 .../{ => sourcedata}/sub-01/fmap/sub-01_B1map.json | 0 .../sourcedata/sub-01/fmap/sub-01_B1map.nii.gz} | 0 .../sub-01/anat/sub-01_MTsat.json} | 0 .../sub-01/anat/sub-01_MTsat.nii.gz} | Bin .../sub-01/anat}/sub-01_PDmap.json | 0 .../sub-01/anat}/sub-01_PDmap.nii.gz | Bin .../sub-01/anat}/sub-01_R1map.json | 0 .../sub-01/anat}/sub-01_R1map.nii.gz | Bin .../sub-01/anat}/sub-01_R2starmap.json | 0 .../sub-01/anat}/sub-01_R2starmap.nii.gz | Bin .../sub-01/fmap}/sub-01_B0map.json | 0 .../sub-01/fmap}/sub-01_B1map.json | 0 .../{ => sourcedata}/sub-01/anat/sub-01_MTw.json | 0 .../{ => sourcedata}/sub-01/anat/sub-01_PDw.json | 0 .../{ => sourcedata}/sub-01/anat/sub-01_T1w.json | 0 .../sub-01/anat/sub-01_echo-1_MTw.json | 0 .../sub-01/anat/sub-01_echo-1_PDw.json | 0 .../sub-01/anat/sub-01_echo-1_T1w.json | 0 .../sub-01/anat/sub-01_echo-1_part-mag_MTw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-1_part-mag_PDw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-1_part-mag_T1w.nii.gz} | Bin .../sub-01/anat/sub-01_echo-2_MTw.json | 0 .../sub-01/anat/sub-01_echo-2_PDw.json | 0 .../sub-01/anat/sub-01_echo-2_T1w.json | 0 .../sub-01/anat/sub-01_echo-2_part-mag_MTw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-2_part-mag_PDw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-2_part-mag_T1w.nii.gz} | Bin .../sub-01/anat/sub-01_echo-3_MTw.json | 0 .../sub-01/anat/sub-01_echo-3_PDw.json | 0 .../sub-01/anat/sub-01_echo-3_T1w.json | 0 .../sub-01/anat/sub-01_echo-3_part-mag_MTw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-3_part-mag_PDw.nii.gz} | Bin .../anat/sub-01_echo-3_part-mag_T1w.nii.gz.gz} | Bin .../sub-01/anat/sub-01_echo-4_MTw.json | 0 .../sub-01/anat/sub-01_echo-4_PDw.json | 0 .../sub-01/anat/sub-01_echo-4_T1w.json | 0 .../sub-01/anat/sub-01_echo-4_part-mag_MTw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-4_part-mag_PDw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-4_part-mag_T1w.nii.gz} | Bin .../sub-01/anat/sub-01_echo-5_MTw.json | 0 .../sub-01/anat/sub-01_echo-5_PDw.json | 0 .../sub-01/anat/sub-01_echo-5_T1w.json | 0 .../sub-01/anat/sub-01_echo-5_part-mag_MTw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-5_part-mag_PDw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-5_part-mag_T1w.nii.gz} | Bin .../sub-01/anat/sub-01_echo-6_MTw.json | 0 .../sub-01/anat/sub-01_echo-6_PDw.json | 0 .../sub-01/anat/sub-01_echo-6_T1w.json | 0 .../sub-01/anat/sub-01_echo-6_part-mag_MTw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-6_part-mag_PDw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-6_part-mag_T1w.nii.gz} | Bin .../sub-01/anat/sub-01_echo-7_PDw.json | 0 .../sub-01/anat/sub-01_echo-7_part-mag_PDw.nii.gz} | Bin .../sub-01/anat/sub-01_echo-8_PDw.json | 0 .../sub-01/anat/sub-01_echo-8_part-mag_PDw.nii.gz} | Bin .../sub-01/fmap/sub-01_B1minusmap_MTw.gz | Bin .../sub-01/fmap/sub-01_B1minusmap_MTw.json | 0 .../sub-01/fmap/sub-01_B1minusmap_PDw.gz | Bin .../sub-01/fmap/sub-01_B1minusmap_PDw.json | 0 .../sub-01/fmap/sub-01_B1minusmap_T1w.gz | Bin .../sub-01/fmap/sub-01_B1minusmap_T1w.json | 0 .../sub-01/fmap/sub-01_echo-1_B1map.json | 0 .../sub-01/fmap/sub-01_echo-1_B1map.nii.gz | Bin .../sub-01/fmap/sub-01_echo-1_part-mag_B0map.json | 0 .../sub-01/fmap/sub-01_echo-1_part-mag_B0map.nii.gz | Bin .../sub-01/fmap/sub-01_echo-2_B1map.json | 0 .../sub-01/fmap/sub-01_echo-2_B1map.nii.gz | Bin .../sub-01/fmap/sub-01_echo-2_part-mag_B0map.json | 0 .../sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz | Bin .../sub-01/fmap/sub-01_echo-2_part-phase_B0map.json | 0 .../fmap/sub-01_echo-2_part-phase_B0map.nii.gz | Bin 120 files changed, 0 insertions(+), 0 deletions(-) rename examples/ds-01/{ => derivatives}/sub-01/anat/sub-01_QSM.json (100%) rename examples/ds-01/{ => derivatives}/sub-01/anat/sub-01_QSM.nii.gz (100%) rename examples/ds-01/{ => derivatives}/sub-01/anat/sub-01_T2starmap.json (100%) rename examples/{ds-03 => ds-01/derivatives}/sub-01/anat/sub-01_T2starmap.nii.gz (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_FLASH.json (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-1_FLASH.json (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-1_part-phase_FLASH.nii.gz (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-2_FLASH.json (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-2_part-mag_FLASH.nii.gz (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-2_part-phase_FLASH.nii.gz (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-3_FLASH.json (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-3_part-mag_FLASH.nii.gz (100%) rename examples/ds-01/{ => sourcedata}/sub-01/anat/sub-01_echo-3_part-phase_FLASH.nii.gz (100%) rename examples/ds-02/{ => derivatives}/sub-01/anat/sub-01_T1map.json (100%) rename examples/ds-02/{ => derivatives}/sub-01/anat/sub-01_T1map.nii.gz (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_MP2RAGE.json (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_T1w.json (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_T1w.nii.gz (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_inv-1_MP2RAGE.json (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_inv-2_MP2RAGE.json (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_inv-2_part-mag_MP2RAGE.nii.gz (100%) rename examples/ds-02/{ => sourcedata}/sub-01/anat/sub-01_inv-2_part-phase_MP2RAGE.nii.gz (100%) rename examples/ds-03/{ => derivatives}/sub-01/anat/sub-01_T1map.json (100%) rename examples/ds-03/{ => derivatives}/sub-01/anat/sub-01_T1map.nii.gz (100%) rename examples/ds-03/{ => derivatives}/sub-01/anat/sub-01_T2starmap.json (100%) rename examples/ds-03/{sub-01/anat/json.tool => derivatives/sub-01/anat/sub-01_T2starmap.nii.gz} (100%) rename examples/ds-03/{sub-01/anat/sub-01_T1w.nii.gz => sourcedata/sub-01/anat/json.tool} (100%) rename examples/ds-03/{ => sourcedata}/sub-01/anat/sub-01_MP2RAGE.json (100%) rename examples/ds-03/{ => sourcedata}/sub-01/anat/sub-01_T1w.json (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_T1w.nii.gz} (100%) rename examples/ds-03/{ => sourcedata}/sub-01/anat/sub-01_inv-1_MP2RAGE.json (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-2_echo-1_part-mag_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{ => sourcedata}/sub-01/anat/sub-01_inv-2_MP2RAGE.json (100%) rename examples/ds-03/{ => sourcedata}/sub-01/anat/sub-01_inv-2_echo-1_MP2RAGE.json (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-2_echo-1_part-phase_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-2_echo-1_part-mag_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-2_echo-2_part-mag_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-2_echo-1_part-phase_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{ => sourcedata}/sub-01/anat/sub-01_inv-2_echo-2_MP2RAGE.json (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-2_echo-2_part-phase_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-2_echo-2_part-mag_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-2_echo-3_part-mag_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-2_echo-2_part-phase_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{ => sourcedata}/sub-01/anat/sub-01_inv-2_echo-3_MP2RAGE.json (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-2_echo-3_part-phase_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-2_echo-3_part-mag_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-2_echo-4_part-mag_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-2_echo-3_part-phase_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{ => sourcedata}/sub-01/anat/sub-01_inv-2_echo-4_MP2RAGE.json (100%) rename examples/ds-03/{sub-01/anat/sub-01_inv-2_echo-4_part-phase_MP2RAGE.nii.gz => sourcedata/sub-01/anat/sub-01_inv-2_echo-4_part-mag_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{sub-01/fmap/sub-01_B1map.nii.gz => sourcedata/sub-01/anat/sub-01_inv-2_echo-4_part-phase_MP2RAGE.nii.gz} (100%) rename examples/ds-03/{ => sourcedata}/sub-01/fmap/sub-01_B1map.json (100%) rename examples/{ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json => ds-03/sourcedata/sub-01/fmap/sub-01_B1map.nii.gz} (100%) rename examples/ds-04/{sub-01/derivatives/sub-01_MTmap.json => derivatives/sub-01/anat/sub-01_MTsat.json} (100%) rename examples/ds-04/{sub-01/anat/sub-01_echo-1_part-mag_MTw.nii.gz => derivatives/sub-01/anat/sub-01_MTsat.nii.gz} (100%) rename examples/ds-04/{sub-01/derivatives => derivatives/sub-01/anat}/sub-01_PDmap.json (100%) rename examples/ds-04/{sub-01/derivatives => derivatives/sub-01/anat}/sub-01_PDmap.nii.gz (100%) rename examples/ds-04/{sub-01/derivatives => derivatives/sub-01/anat}/sub-01_R1map.json (100%) rename examples/ds-04/{sub-01/derivatives => derivatives/sub-01/anat}/sub-01_R1map.nii.gz (100%) rename examples/ds-04/{sub-01/derivatives => derivatives/sub-01/anat}/sub-01_R2starmap.json (100%) rename examples/ds-04/{sub-01/derivatives => derivatives/sub-01/anat}/sub-01_R2starmap.nii.gz (100%) rename examples/ds-04/{sub-01/derivatives => derivatives/sub-01/fmap}/sub-01_B0map.json (100%) rename examples/ds-04/{sub-01/derivatives => derivatives/sub-01/fmap}/sub-01_B1map.json (100%) rename examples/ds-04/{ => sourcedata}/sub-01/anat/sub-01_MTw.json (100%) rename examples/ds-04/{ => sourcedata}/sub-01/anat/sub-01_PDw.json (100%) rename examples/ds-04/{ => sourcedata}/sub-01/anat/sub-01_T1w.json (100%) rename examples/ds-04/{ => sourcedata}/sub-01/anat/sub-01_echo-1_MTw.json (100%) rename examples/ds-04/{ => sourcedata}/sub-01/anat/sub-01_echo-1_PDw.json (100%) rename examples/ds-04/{ => sourcedata}/sub-01/anat/sub-01_echo-1_T1w.json (100%) rename examples/ds-04/{sub-01/anat/sub-01_echo-1_part-mag_PDw.nii.gz => sourcedata/sub-01/anat/sub-01_echo-1_part-mag_MTw.nii.gz} (100%) rename examples/ds-04/{sub-01/anat/sub-01_echo-1_part-mag_T1w.nii.gz => sourcedata/sub-01/anat/sub-01_echo-1_part-mag_PDw.nii.gz} (100%) rename examples/ds-04/{sub-01/anat/sub-01_echo-2_part-mag_MTw.nii.gz => sourcedata/sub-01/anat/sub-01_echo-1_part-mag_T1w.nii.gz} (100%) rename examples/ds-04/{ => sourcedata}/sub-01/anat/sub-01_echo-2_MTw.json (100%) rename examples/ds-04/{ => sourcedata}/sub-01/anat/sub-01_echo-2_PDw.json (100%) rename examples/ds-04/{ => 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examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz From 6b7d1c84dc19ba385a6a3f5da69853847e7f90f1 Mon Sep 17 00:00:00 2001 From: Kirstie Whitaker Date: Mon, 15 Apr 2019 21:11:04 +0100 Subject: [PATCH 03/14] Move example RAW data from SOURCE data --- .../{sourcedata => }/sub-01/anat/sub-01_FLASH.json | 0 .../sub-01/anat/sub-01_echo-1_FLASH.json | 0 .../sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-1_part-phase_FLASH.nii.gz | 0 .../sub-01/anat/sub-01_echo-2_FLASH.json | 0 .../sub-01/anat/sub-01_echo-2_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-2_part-phase_FLASH.nii.gz | 0 .../sub-01/anat/sub-01_echo-3_FLASH.json | 0 .../sub-01/anat/sub-01_echo-3_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-3_part-phase_FLASH.nii.gz | 0 .../sub-01/anat/sub-01_MP2RAGE.json | 0 .../{sourcedata => }/sub-01/anat/sub-01_T1w.json | 0 .../{sourcedata => }/sub-01/anat/sub-01_T1w.nii.gz | 0 .../sub-01/anat/sub-01_inv-1_MP2RAGE.json | 0 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diff --git a/examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_B1map.nii.gz b/examples/ds-04/sub-01/fmap/sub-01_echo-2_B1map.nii.gz similarity index 100% rename from examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_B1map.nii.gz rename to examples/ds-04/sub-01/fmap/sub-01_echo-2_B1map.nii.gz diff --git a/examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json b/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json similarity index 100% rename from examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json rename to examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json diff --git a/examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz b/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz similarity index 100% rename from examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz rename to examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz diff --git a/examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json b/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json similarity index 100% rename from examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json rename to examples/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json diff --git a/examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz b/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz similarity index 100% rename from examples/ds-04/sourcedata/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz rename to examples/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz From b140377c94454cae32ebcaeee1537ef27a8711c4 Mon Sep 17 00:00:00 2001 From: Kirstie Whitaker Date: Mon, 15 Apr 2019 21:34:31 +0100 Subject: [PATCH 04/14] Move derivatives files in ds-4 to an hmri pipeline folder --- .../{ => hmri}/sub-01/anat/sub-01_MTsat.json | 0 .../{ => hmri}/sub-01/anat/sub-01_MTsat.nii.gz | Bin .../{ => hmri}/sub-01/anat/sub-01_PDmap.json | 0 .../{ => hmri}/sub-01/anat/sub-01_PDmap.nii.gz | Bin .../{ => hmri}/sub-01/anat/sub-01_R1map.json | 0 .../{ => hmri}/sub-01/anat/sub-01_R1map.nii.gz | Bin .../{ => hmri}/sub-01/anat/sub-01_R2starmap.json | 0 .../{ => hmri}/sub-01/anat/sub-01_R2starmap.nii.gz | Bin .../{ => hmri}/sub-01/fmap/sub-01_B0map.json | 0 .../{ => hmri}/sub-01/fmap/sub-01_B1map.json | 0 10 files changed, 0 insertions(+), 0 deletions(-) rename examples/ds-04/derivatives/{ => hmri}/sub-01/anat/sub-01_MTsat.json (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/anat/sub-01_MTsat.nii.gz (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/anat/sub-01_PDmap.json (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/anat/sub-01_PDmap.nii.gz (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/anat/sub-01_R1map.json (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/anat/sub-01_R1map.nii.gz (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/anat/sub-01_R2starmap.json (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/anat/sub-01_R2starmap.nii.gz (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/fmap/sub-01_B0map.json (100%) rename examples/ds-04/derivatives/{ => hmri}/sub-01/fmap/sub-01_B1map.json (100%) diff --git a/examples/ds-04/derivatives/sub-01/anat/sub-01_MTsat.json b/examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_MTsat.json similarity index 100% rename from examples/ds-04/derivatives/sub-01/anat/sub-01_MTsat.json rename to examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_MTsat.json diff --git a/examples/ds-04/derivatives/sub-01/anat/sub-01_MTsat.nii.gz b/examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_MTsat.nii.gz similarity index 100% rename from examples/ds-04/derivatives/sub-01/anat/sub-01_MTsat.nii.gz rename to examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_MTsat.nii.gz diff --git a/examples/ds-04/derivatives/sub-01/anat/sub-01_PDmap.json b/examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_PDmap.json similarity index 100% rename from examples/ds-04/derivatives/sub-01/anat/sub-01_PDmap.json rename to examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_PDmap.json diff --git a/examples/ds-04/derivatives/sub-01/anat/sub-01_PDmap.nii.gz b/examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_PDmap.nii.gz similarity index 100% rename from examples/ds-04/derivatives/sub-01/anat/sub-01_PDmap.nii.gz rename to examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_PDmap.nii.gz diff --git a/examples/ds-04/derivatives/sub-01/anat/sub-01_R1map.json b/examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_R1map.json similarity index 100% rename from examples/ds-04/derivatives/sub-01/anat/sub-01_R1map.json rename to examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_R1map.json diff --git a/examples/ds-04/derivatives/sub-01/anat/sub-01_R1map.nii.gz b/examples/ds-04/derivatives/hmri/sub-01/anat/sub-01_R1map.nii.gz similarity index 100% rename from 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to examples/ds-04/derivatives/hmri/sub-01/fmap/sub-01_B0map.json diff --git a/examples/ds-04/derivatives/sub-01/fmap/sub-01_B1map.json b/examples/ds-04/derivatives/hmri/sub-01/fmap/sub-01_B1map.json similarity index 100% rename from examples/ds-04/derivatives/sub-01/fmap/sub-01_B1map.json rename to examples/ds-04/derivatives/hmri/sub-01/fmap/sub-01_B1map.json From 2cc6d070bb62accce5cab01734ad3488327825e8 Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Fri, 19 Apr 2019 15:28:21 +0100 Subject: [PATCH 05/14] Made clearer names for "ds-01/2/3/4" folders; pipeline names in derivative folder; markdown file to introduce the Examples branch --- examples/BEP001_examples.md | 21 ++++++++++++++++++ .../dataset_description.json | 2 +- .../qsm_pipeline}/sub-01/anat/sub-01_QSM.json | 0 .../sub-01/anat/sub-01_QSM.nii.gz | 0 .../sub-01/anat/sub-01_T2starmap.json | 0 .../sub-01/anat/sub-01_T2starmap.nii.gz | 0 .../sub-01/anat/sub-01_FLASH.json | 0 .../sub-01/anat/sub-01_echo-1_FLASH.json | 0 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additions/changes that it brings to the BIDS format, here: https://github.com/bids-standard/bep001. + + *The datasets in this branch contain empty data files, which might be useful for building simple software tests. + The current branch may eventually be merged with the bids-examples branch of the main bids-standard repo: https://github.com/bids-standard/bids-examples, in which case this disclaimer will be redundant.* + + +## Example 1: MEGRE, multi-echo +This is a sample dataset from a single MEGRE sequence, which yields multiple images, corresponding to different echo times. This dataset has been used to calculate a quantitative susceptibility map (QSM), as well as a T2* map. + +## Example 2: MP2RAGE, single echo +This is a sample dataset from a standard MP2RAGE sequence, which includes two GRE images acquired after a single inversion pulse. This data have been used to create a T1-map, as well as a T1-weighted image, corrected for B0 and B1-inhomogeneities, which are both part of the example dataset. + +## Example 3: MP2RAGE, multi-echo +This is a sample dataset from an MP2RAGE sequence with two inversion times, and, for the second inversion time, 4 different echoes. + +## Example 4: MultiParameter Mapping (MPM) dataset +This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle. \ No newline at end of file diff --git a/examples/ds-01/dataset_description.json b/examples/MEGRE_multiecho/dataset_description.json similarity index 84% rename from examples/ds-01/dataset_description.json rename to examples/MEGRE_multiecho/dataset_description.json index a6b88d7..7baebeb 100644 --- a/examples/ds-01/dataset_description.json +++ b/examples/MEGRE_multiecho/dataset_description.json @@ -5,5 +5,5 @@ "Kirstie Whitaker", "Gilles de Hollander" ], - "Description": "This virtual dataset is collected using a single FLASH sequence, which yields multiple images, corresponding to different echo times. This data has been used to calculate a quantitative susceptibility map, as well as a T2* map." + "Description": "This virtual dataset is collected using a single MEGRE sequence, which yields multiple images, corresponding to different echo times. This data has been used to calculate a quantitative susceptibility map, as well as a T2* map." } diff --git a/examples/ds-01/derivatives/sub-01/anat/sub-01_QSM.json b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json similarity index 100% rename from examples/ds-01/derivatives/sub-01/anat/sub-01_QSM.json rename to examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json diff --git a/examples/ds-01/derivatives/sub-01/anat/sub-01_QSM.nii.gz b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.nii.gz similarity index 100% rename from examples/ds-01/derivatives/sub-01/anat/sub-01_QSM.nii.gz rename to examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.nii.gz diff --git a/examples/ds-01/derivatives/sub-01/anat/sub-01_T2starmap.json b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json similarity index 100% rename from examples/ds-01/derivatives/sub-01/anat/sub-01_T2starmap.json rename to examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json diff --git a/examples/ds-01/derivatives/sub-01/anat/sub-01_T2starmap.nii.gz b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.nii.gz similarity index 100% rename from examples/ds-01/derivatives/sub-01/anat/sub-01_T2starmap.nii.gz rename to examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.nii.gz diff --git a/examples/ds-01/sub-01/anat/sub-01_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_FLASH.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_FLASH.json rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_FLASH.json diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-1_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_FLASH.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-1_FLASH.json rename to 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from examples/ds-04/sub-01/fmap/sub-01_B1minusmap_T1w.gz rename to examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.gz diff --git a/examples/ds-04/sub-01/fmap/sub-01_B1minusmap_T1w.json b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.json similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_B1minusmap_T1w.json rename to examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.json diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-1_B1map.json b/examples/MPM/sub-01/fmap/sub-01_echo-1_B1map.json similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_echo-1_B1map.json rename to examples/MPM/sub-01/fmap/sub-01_echo-1_B1map.json diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-1_B1map.nii.gz b/examples/MPM/sub-01/fmap/sub-01_echo-1_B1map.nii.gz similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_echo-1_B1map.nii.gz rename to examples/MPM/sub-01/fmap/sub-01_echo-1_B1map.nii.gz diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-1_part-mag_B0map.json 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examples/ds-04/sub-01/fmap/sub-01_echo-2_B1map.nii.gz rename to examples/MPM/sub-01/fmap/sub-01_echo-2_B1map.nii.gz diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json rename to examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz rename to examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json rename to examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz similarity index 100% rename from examples/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz rename to examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz From 2c716cdfdeb4534d4469f9910a3fe03a2d0b389b Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Mon, 22 Apr 2019 13:41:32 +0100 Subject: [PATCH 06/14] Integrated suggested explanation for avoiding FLASH/MEGRE suffix in the MPM example --- examples/BEP001_examples.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/examples/BEP001_examples.md b/examples/BEP001_examples.md index 528b6a5..75d1410 100644 --- a/examples/BEP001_examples.md +++ b/examples/BEP001_examples.md @@ -18,4 +18,5 @@ This is a sample dataset from a standard MP2RAGE sequence, which includes two GR This is a sample dataset from an MP2RAGE sequence with two inversion times, and, for the second inversion time, 4 different echoes. ## Example 4: MultiParameter Mapping (MPM) dataset -This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle. \ No newline at end of file +This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle. +Note that the raw data for these scans are not called "FLASH" (or MEGRE, following our recommended vendor-neutral notation) in their suffices, rather they are grouped together with the "MPM" suffix and the "acq" tag is used to clarify which weightings the scans are highlighting. From 33f69cb31cede0398defaa471d02e32427ec9462 Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Tue, 28 May 2019 19:30:23 +0100 Subject: [PATCH 07/14] Fixed MPM and MEGRE examples, added sequence suffix to raw data --- .../sub-01/anat/sub-01_FLASH.json | 5 ----- .../sub-01/anat/sub-01_MEGRE.json | 0 .../sub-01/anat/sub-01_echo-1_FLASH.json | 3 --- .../sub-01/anat/sub-01_echo-1_MEGRE.json | 0 .../anat/sub-01_echo-1_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-1_part-mag_MEGRE.nii.gz | 0 .../anat/sub-01_echo-1_part-phase_FLASH.nii.gz | 0 .../anat/sub-01_echo-1_part-phase_MEGRE.nii.gz | 0 .../sub-01/anat/sub-01_echo-2_FLASH.json | 3 --- .../sub-01/anat/sub-01_echo-2_MEGRE.json | 0 .../anat/sub-01_echo-2_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-2_part-mag_MEGRE.nii.gz | 0 .../anat/sub-01_echo-2_part-phase_FLASH.nii.gz | 0 .../anat/sub-01_echo-2_part-phase_MEGRE.nii.gz | 0 .../sub-01/anat/sub-01_echo-3_FLASH.json | 3 --- .../sub-01/anat/sub-01_echo-3_MEGRE.json | 0 .../anat/sub-01_echo-3_part-mag_FLASH.nii.gz | 0 .../anat/sub-01_echo-3_part-mag_MEGRE.nii.gz | 0 .../anat/sub-01_echo-3_part-phase_FLASH.nii.gz | 0 .../anat/sub-01_echo-3_part-phase_MEGRE.nii.gz | 0 .../hmri/sub-01/fmap/sub-01_B0map.gz} | Bin .../hmri/sub-01/fmap/sub-01_B1map.nii.gz} | Bin ...ub-01_MTw.json => sub-01_acq-MToff_MPM.json} | 0 ...sub-01_PDw.json => sub-01_acq-MTon_MPM.json} | 0 ...{sub-01_T1w.json => sub-01_acq-T1w_MPM.json} | 0 ...Tw.json => sub-01_echo-1_acq-MToff_MPM.json} | 0 ...PDw.json => sub-01_echo-1_acq-MTon_MPM.json} | 0 ..._T1w.json => sub-01_echo-1_acq-T1w_MPM.json} | 0 ...ub-01_echo-1_part-mag__acq-MToff_MPM.nii.gz} | Bin ... sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz} | Bin ...> sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz} | Bin ...Tw.json => sub-01_echo-2_acq-MToff_MPM.json} | 0 ...PDw.json => sub-01_echo-2_acq-MTon_MPM.json} | 0 ..._T1w.json => sub-01_echo-2_acq-T1w_MPM.json} | 0 ...sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz} | Bin ... sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz} | Bin ...> sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz} | Bin ...Tw.json => sub-01_echo-3_acq-MToff_MPM.json} | 0 ...PDw.json => sub-01_echo-3_acq-MTon_MPM.json} | 0 ..._T1w.json => sub-01_echo-3_acq-T1w_MPM.json} | 0 ...sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz} | Bin ... sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz} | Bin ...ub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz.gz} | Bin ...Tw.json => sub-01_echo-4_acq-MToff_MPM.json} | 0 ...PDw.json => sub-01_echo-4_acq-MTon_MPM.json} | 0 ..._T1w.json => sub-01_echo-4_acq-T1w_MPM.json} | 0 ...sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz} | Bin ... sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz} | Bin ...> sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz} | Bin ...Tw.json => sub-01_echo-5_acq-MToff_MPM.json} | 0 ...PDw.json => sub-01_echo-5_acq-MTon_MPM.json} | 0 ..._T1w.json => sub-01_echo-5_acq-T1w_MPM.json} | 0 ...sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz} | Bin ... sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz} | Bin ...> sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz} | Bin ...Tw.json => sub-01_echo-6_acq-MToff_MPM.json} | 0 ...PDw.json => sub-01_echo-6_acq-MTon_MPM.json} | 0 ..._T1w.json => sub-01_echo-6_acq-T1w_MPM.json} | 0 ...sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz} | Bin ... sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz} | Bin ...> sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz} | Bin ...Dw.json => sub-01_echo-7_acq-MToff_MPM.json} | 0 .../sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz | Bin 0 -> 81872 bytes ...Dw.json => sub-01_echo-8_acq-MToff_MPM.json} | 0 .../sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz | Bin 0 -> 81872 bytes .../anat/sub-01_echo-1_inv-2_MP2RAGE.json | 3 --- .../sub-01_echo-1_inv-2_part-mag_MP2RAGE.nii.gz | 0 ...ub-01_echo-1_inv-2_part-phase_MP2RAGE.nii.gz | 0 .../anat/sub-01_echo-2_inv-2_MP2RAGE.json | 3 --- .../sub-01_echo-2_inv-2_part-mag_MP2RAGE.nii.gz | 0 ...ub-01_echo-2_inv-2_part-phase_MP2RAGE.nii.gz | 0 .../anat/sub-01_echo-3_inv-2_MP2RAGE.json | 3 --- .../sub-01_echo-3_inv-2_part-mag_MP2RAGE.nii.gz | 0 ...ub-01_echo-3_inv-2_part-phase_MP2RAGE.nii.gz | 0 .../anat/sub-01_echo-4_inv-2_MP2RAGE.json | 3 --- .../sub-01_echo-4_inv-2_part-mag_MP2RAGE.nii.gz | 0 ...ub-01_echo-4_inv-2_part-phase_MP2RAGE.nii.gz | 0 77 files changed, 26 deletions(-) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_FLASH.json rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_MEGRE.json (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_FLASH.json rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-1_MEGRE.json (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-1_part-mag_MEGRE.nii.gz (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-phase_FLASH.nii.gz rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-1_part-phase_MEGRE.nii.gz (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_FLASH.json rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-2_MEGRE.json (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-mag_FLASH.nii.gz rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-2_part-mag_MEGRE.nii.gz (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-phase_FLASH.nii.gz rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-2_part-phase_MEGRE.nii.gz (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_FLASH.json rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-3_MEGRE.json (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-mag_FLASH.nii.gz rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-3_part-mag_MEGRE.nii.gz (100%) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-phase_FLASH.nii.gz rename examples/{ds-01 => MEGRE_multiecho}/sub-01/anat/sub-01_echo-3_part-phase_MEGRE.nii.gz (100%) rename examples/MPM/{sub-01/anat/sub-01_echo-1_part-mag_MTw.nii.gz => derivatives/hmri/sub-01/fmap/sub-01_B0map.gz} (100%) rename examples/MPM/{sub-01/anat/sub-01_echo-1_part-mag_PDw.nii.gz => derivatives/hmri/sub-01/fmap/sub-01_B1map.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_MTw.json => sub-01_acq-MToff_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_PDw.json => sub-01_acq-MTon_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_T1w.json => sub-01_acq-T1w_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-1_MTw.json => sub-01_echo-1_acq-MToff_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-1_PDw.json => sub-01_echo-1_acq-MTon_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-1_T1w.json => sub-01_echo-1_acq-T1w_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-1_part-mag_T1w.nii.gz => sub-01_echo-1_part-mag__acq-MToff_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-2_part-mag_MTw.nii.gz => sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-2_part-mag_PDw.nii.gz => sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-2_MTw.json => sub-01_echo-2_acq-MToff_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-2_PDw.json => sub-01_echo-2_acq-MTon_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-2_T1w.json => sub-01_echo-2_acq-T1w_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-2_part-mag_T1w.nii.gz => sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-3_part-mag_MTw.nii.gz => sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-3_part-mag_PDw.nii.gz => sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-3_MTw.json => sub-01_echo-3_acq-MToff_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-3_PDw.json => sub-01_echo-3_acq-MTon_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-3_T1w.json => sub-01_echo-3_acq-T1w_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-3_part-mag_T1w.nii.gz.gz => sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-4_part-mag_MTw.nii.gz => sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-4_part-mag_PDw.nii.gz => sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-4_MTw.json => sub-01_echo-4_acq-MToff_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-4_PDw.json => sub-01_echo-4_acq-MTon_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-4_T1w.json => sub-01_echo-4_acq-T1w_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-4_part-mag_T1w.nii.gz => sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-5_part-mag_MTw.nii.gz => sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-5_part-mag_PDw.nii.gz => sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-5_MTw.json => sub-01_echo-5_acq-MToff_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-5_PDw.json => sub-01_echo-5_acq-MTon_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-5_T1w.json => sub-01_echo-5_acq-T1w_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-5_part-mag_T1w.nii.gz => sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-6_part-mag_MTw.nii.gz => sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-6_part-mag_PDw.nii.gz => sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-6_MTw.json => sub-01_echo-6_acq-MToff_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-6_PDw.json => sub-01_echo-6_acq-MTon_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-6_T1w.json => sub-01_echo-6_acq-T1w_MPM.json} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-6_part-mag_T1w.nii.gz => sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-7_part-mag_PDw.nii.gz => sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-8_part-mag_PDw.nii.gz => sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-7_PDw.json => sub-01_echo-7_acq-MToff_MPM.json} (100%) create mode 100644 examples/MPM/sub-01/anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz rename examples/MPM/sub-01/anat/{sub-01_echo-8_PDw.json => sub-01_echo-8_acq-MToff_MPM.json} (100%) create mode 100644 examples/MPM/sub-01/anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_MP2RAGE.json delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-mag_MP2RAGE.nii.gz delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-phase_MP2RAGE.nii.gz delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_MP2RAGE.json delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-mag_MP2RAGE.nii.gz delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-phase_MP2RAGE.nii.gz delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_MP2RAGE.json delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-mag_MP2RAGE.nii.gz delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-phase_MP2RAGE.nii.gz delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_MP2RAGE.json delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-mag_MP2RAGE.nii.gz delete mode 100644 examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-phase_MP2RAGE.nii.gz diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_FLASH.json deleted file mode 100644 index ba52a97..0000000 --- a/examples/MEGRE_multiecho/sub-01/anat/sub-01_FLASH.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "MagneticFieldStrength": 7, - "RepetitionTimeExcitation": 0.04, - "FlipAngle": 14 -} diff --git a/examples/ds-01/sub-01/anat/sub-01_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_MEGRE.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_MEGRE.json rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_MEGRE.json diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_FLASH.json deleted file mode 100644 index 755f482..0000000 --- a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_FLASH.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.01 -} diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-1_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-1_MEGRE.json rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-mag_FLASH.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-1_part-mag_MEGRE.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-mag_MEGRE.nii.gz similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-1_part-mag_MEGRE.nii.gz rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-mag_MEGRE.nii.gz diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-phase_FLASH.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-phase_FLASH.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-1_part-phase_MEGRE.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-phase_MEGRE.nii.gz similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-1_part-phase_MEGRE.nii.gz rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_part-phase_MEGRE.nii.gz diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_FLASH.json deleted file mode 100644 index 3d2e5b4..0000000 --- a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_FLASH.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.02 -} diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-2_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-2_MEGRE.json rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-mag_FLASH.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-mag_FLASH.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-2_part-mag_MEGRE.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-mag_MEGRE.nii.gz similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-2_part-mag_MEGRE.nii.gz rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-mag_MEGRE.nii.gz diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-phase_FLASH.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-phase_FLASH.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-2_part-phase_MEGRE.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-phase_MEGRE.nii.gz similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-2_part-phase_MEGRE.nii.gz rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_part-phase_MEGRE.nii.gz diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_FLASH.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_FLASH.json deleted file mode 100644 index 6928485..0000000 --- a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_FLASH.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.03 -} diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-3_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-3_MEGRE.json rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-mag_FLASH.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-mag_FLASH.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-3_part-mag_MEGRE.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-mag_MEGRE.nii.gz similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-3_part-mag_MEGRE.nii.gz rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-mag_MEGRE.nii.gz diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-phase_FLASH.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-phase_FLASH.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-3_part-phase_MEGRE.nii.gz b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-phase_MEGRE.nii.gz similarity index 100% rename from examples/ds-01/sub-01/anat/sub-01_echo-3_part-phase_MEGRE.nii.gz rename to examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_part-phase_MEGRE.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_MTw.nii.gz b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_MTw.nii.gz rename to examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_PDw.nii.gz b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1map.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_PDw.nii.gz rename to examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1map.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_MTw.json b/examples/MPM/sub-01/anat/sub-01_acq-MToff_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_MTw.json rename to examples/MPM/sub-01/anat/sub-01_acq-MToff_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_PDw.json 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a/examples/MPM/sub-01/anat/sub-01_echo-1_T1w.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-1_T1w.json rename to examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_T1w.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-1_part-mag__acq-MToff_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_T1w.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-1_part-mag__acq-MToff_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_MTw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_MTw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_PDw.nii.gz 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--git a/examples/MPM/sub-01/anat/sub-01_echo-3_MTw.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-3_MTw.json rename to examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_PDw.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-3_PDw.json rename to examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_T1w.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-3_T1w.json rename to examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_T1w.nii.gz.gz b/examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz similarity index 100% rename from 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examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_PDw.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-4_PDw.json rename to examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_T1w.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-4_T1w.json rename to examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_part-mag_T1w.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-4_part-mag_T1w.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_MTw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_MTw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_PDw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_PDw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_MTw.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-5_MTw.json rename to examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_PDw.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-5_PDw.json rename to examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_T1w.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-5_T1w.json rename to examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_T1w.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_T1w.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_MTw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_MTw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_PDw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_PDw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_MTw.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-6_MTw.json rename to examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_PDw.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-6_PDw.json rename to examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_T1w.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-6_T1w.json rename to examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_T1w.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_T1w.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-7_part-mag_PDw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-7_part-mag_PDw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-8_part-mag_PDw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz similarity index 100% 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pPBNR0tXwen<`5u2fB*pk1PBlyK!5;&|08g}b*fOjo!_u<(O+7w*9-sv literal 0 HcmV?d00001 diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_MP2RAGE.json b/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_MP2RAGE.json deleted file mode 100644 index 6e56745..0000000 --- a/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_MP2RAGE.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.006 -} diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-mag_MP2RAGE.nii.gz b/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-mag_MP2RAGE.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-phase_MP2RAGE.nii.gz b/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-phase_MP2RAGE.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_MP2RAGE.json b/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_MP2RAGE.json deleted file mode 100644 index d257a48..0000000 --- a/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_MP2RAGE.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.0145 -} diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-mag_MP2RAGE.nii.gz b/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-mag_MP2RAGE.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-phase_MP2RAGE.nii.gz b/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-phase_MP2RAGE.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_MP2RAGE.json b/examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_MP2RAGE.json deleted file mode 100644 index 878ae21..0000000 --- a/examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_MP2RAGE.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.023 -} diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-mag_MP2RAGE.nii.gz b/examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-mag_MP2RAGE.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-phase_MP2RAGE.nii.gz b/examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-phase_MP2RAGE.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_MP2RAGE.json b/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_MP2RAGE.json deleted file mode 100644 index 92a848f..0000000 --- a/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_MP2RAGE.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.0315 -} diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-mag_MP2RAGE.nii.gz b/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-mag_MP2RAGE.nii.gz deleted file mode 100644 index e69de29..0000000 diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-phase_MP2RAGE.nii.gz b/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-phase_MP2RAGE.nii.gz deleted file mode 100644 index e69de29..0000000 From 1ecae5d27439cea2c09c186a8bdb7b72af66410a Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Sun, 15 Sep 2019 18:15:00 +0100 Subject: [PATCH 08/14] Removed extra json files to be compliant with the inheritance principle; fixed suffices --- .../MEGRE_multiecho/sub-01/anat/sub-01_MEGRE.json | 5 ----- examples/MP2RAGE_multiecho/sub-01/anat/json.tool | 0 .../sub-01/anat/sub-01_MP2RAGE.json | 4 ---- .../sub-01/anat/sub-01_inv-1_MP2RAGE.json | 5 ----- .../sub-01/anat/sub-01_MP2RAGE.json | 6 ------ .../fmap/{sub-01_B0map.gz => sub-01_B0map.nii.gz} | Bin .../{sub-01_B1map.json => sub-01_B1plusmap.json} | 0 ...{sub-01_B1map.nii.gz => sub-01_B1plusmap.nii.gz} | Bin examples/MPM/sub-01/anat/sub-01_acq-MToff_MPM.json | 6 ------ examples/MPM/sub-01/anat/sub-01_acq-MTon_MPM.json | 6 ------ examples/MPM/sub-01/anat/sub-01_acq-T1w_MPM.json | 7 ------- .../sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json | 1 - .../MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json | 1 - .../MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json | 1 - ... => sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz} | Bin ...gz => sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz} | Bin ...minusmap_MTw.gz => sub-01_B1minusmap_MTw.nii.gz} | Bin ...minusmap_PDw.gz => sub-01_B1minusmap_PDw.nii.gz} | Bin ...minusmap_T1w.gz => sub-01_B1minusmap_T1w.nii.gz} | Bin ...ho-1_B1map.json => sub-01_echo-1_B1plusmap.json} | 0 ..._B1map.nii.gz => sub-01_echo-1_B1plusmap.nii.gz} | Bin ...ho-2_B1map.json => sub-01_echo-2_B1plusmap.json} | 0 ..._B1map.nii.gz => sub-01_echo-2_B1plusmap.nii.gz} | Bin 23 files changed, 42 deletions(-) delete mode 100644 examples/MEGRE_multiecho/sub-01/anat/sub-01_MEGRE.json delete mode 100644 examples/MP2RAGE_multiecho/sub-01/anat/json.tool delete mode 100644 examples/MP2RAGE_multiecho/sub-01/anat/sub-01_MP2RAGE.json delete mode 100644 examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json delete mode 100644 examples/MP2RAGE_singleecho/sub-01/anat/sub-01_MP2RAGE.json rename examples/MPM/derivatives/hmri/sub-01/fmap/{sub-01_B0map.gz => sub-01_B0map.nii.gz} (100%) rename examples/MPM/derivatives/hmri/sub-01/fmap/{sub-01_B1map.json => sub-01_B1plusmap.json} (100%) rename examples/MPM/derivatives/hmri/sub-01/fmap/{sub-01_B1map.nii.gz => sub-01_B1plusmap.nii.gz} (100%) delete mode 100644 examples/MPM/sub-01/anat/sub-01_acq-MToff_MPM.json delete mode 100644 examples/MPM/sub-01/anat/sub-01_acq-MTon_MPM.json delete mode 100644 examples/MPM/sub-01/anat/sub-01_acq-T1w_MPM.json delete mode 100644 examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json delete mode 100644 examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json delete mode 100644 examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json rename examples/MPM/sub-01/anat/{sub-01_echo-1_part-mag__acq-MToff_MPM.nii.gz => sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz} (100%) rename examples/MPM/sub-01/anat/{sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz.gz => sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz} (100%) rename examples/MPM/sub-01/fmap/{sub-01_B1minusmap_MTw.gz => sub-01_B1minusmap_MTw.nii.gz} (100%) rename examples/MPM/sub-01/fmap/{sub-01_B1minusmap_PDw.gz => sub-01_B1minusmap_PDw.nii.gz} (100%) rename examples/MPM/sub-01/fmap/{sub-01_B1minusmap_T1w.gz => sub-01_B1minusmap_T1w.nii.gz} (100%) rename examples/MPM/sub-01/fmap/{sub-01_echo-1_B1map.json => sub-01_echo-1_B1plusmap.json} (100%) rename examples/MPM/sub-01/fmap/{sub-01_echo-1_B1map.nii.gz => sub-01_echo-1_B1plusmap.nii.gz} (100%) rename examples/MPM/sub-01/fmap/{sub-01_echo-2_B1map.json => sub-01_echo-2_B1plusmap.json} (100%) rename examples/MPM/sub-01/fmap/{sub-01_echo-2_B1map.nii.gz => sub-01_echo-2_B1plusmap.nii.gz} (100%) diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_MEGRE.json deleted file mode 100644 index ba52a97..0000000 --- a/examples/MEGRE_multiecho/sub-01/anat/sub-01_MEGRE.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "MagneticFieldStrength": 7, - "RepetitionTimeExcitation": 0.04, - "FlipAngle": 14 -} diff --git a/examples/MP2RAGE_multiecho/sub-01/anat/json.tool b/examples/MP2RAGE_multiecho/sub-01/anat/json.tool deleted file mode 100644 index e69de29..0000000 diff --git a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_MP2RAGE.json b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_MP2RAGE.json deleted file mode 100644 index 422d114..0000000 --- a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_MP2RAGE.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "NumberShots": 150, - "RepetitionTimeInversion": 6.723 -} diff --git a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json deleted file mode 100644 index 3b2187b..0000000 --- a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "InversionTime": 0.67, - "FlipAngle": 7, - "RepetitionTimeExcitation": 0.0062 -} diff --git a/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_MP2RAGE.json b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_MP2RAGE.json deleted file mode 100644 index 72f72f9..0000000 --- a/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_MP2RAGE.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "MagneticFieldStrength": 7, - "RepetitionTimeExcitation": 0.0062, - "RepetitionTimeInversion": 5.5, - "NumberShots": 159 -} diff --git a/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.gz b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.nii.gz similarity index 100% rename from examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.gz rename to examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.nii.gz diff --git a/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1map.json b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.json similarity index 100% rename from examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1map.json rename to examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.json diff --git a/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1map.nii.gz b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.nii.gz similarity index 100% rename from examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1map.nii.gz rename to examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_acq-MToff_MPM.json deleted file mode 100644 index e1fb09a..0000000 --- a/examples/MPM/sub-01/anat/sub-01_acq-MToff_MPM.json +++ /dev/null @@ -1,6 +0,0 @@ -{"IntendedFor": ["anat/sub-01_PDmap.nii.gz", - "anat/sub-01_MTmap.nii.gz", - "anat/sub-01_R1map.nii.gz", -"anat/sub-01_R2starmap.nii.gz"], -"RepetitionTime": 0.0237, -"FlipAngle": 6} diff --git a/examples/MPM/sub-01/anat/sub-01_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_acq-MTon_MPM.json deleted file mode 100644 index e1fb09a..0000000 --- a/examples/MPM/sub-01/anat/sub-01_acq-MTon_MPM.json +++ /dev/null @@ -1,6 +0,0 @@ -{"IntendedFor": ["anat/sub-01_PDmap.nii.gz", - "anat/sub-01_MTmap.nii.gz", - "anat/sub-01_R1map.nii.gz", -"anat/sub-01_R2starmap.nii.gz"], -"RepetitionTime": 0.0237, -"FlipAngle": 6} diff --git a/examples/MPM/sub-01/anat/sub-01_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_acq-T1w_MPM.json deleted file mode 100644 index 7d4274d..0000000 --- a/examples/MPM/sub-01/anat/sub-01_acq-T1w_MPM.json +++ /dev/null @@ -1,7 +0,0 @@ -{"IntendedFor": ["anat/sub-01_PDmap.nii.gz", - "anat/sub-01_MTmap.nii.gz", - "anat/sub-01_R1map.nii.gz", -"anat/sub-01_R2starmap.nii.gz"], -"RepetitionTime": 0.0187, -"FlipAngle": 20} - diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json deleted file mode 100644 index 417be57..0000000 --- a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json deleted file mode 100644 index 417be57..0000000 --- a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json deleted file mode 100644 index 417be57..0000000 --- a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_part-mag__acq-MToff_MPM.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-1_part-mag__acq-MToff_MPM.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz.gz b/examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz similarity index 100% rename from examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz.gz rename to examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.gz b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.nii.gz similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.gz rename to examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.nii.gz diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.gz b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.nii.gz similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.gz rename to examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.nii.gz diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.gz b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.nii.gz similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.gz rename to examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.nii.gz diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-1_B1map.json b/examples/MPM/sub-01/fmap/sub-01_echo-1_B1plusmap.json similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_echo-1_B1map.json rename to examples/MPM/sub-01/fmap/sub-01_echo-1_B1plusmap.json diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-1_B1map.nii.gz b/examples/MPM/sub-01/fmap/sub-01_echo-1_B1plusmap.nii.gz similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_echo-1_B1map.nii.gz rename to examples/MPM/sub-01/fmap/sub-01_echo-1_B1plusmap.nii.gz diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-2_B1map.json b/examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.json similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_echo-2_B1map.json rename to examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.json diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-2_B1map.nii.gz b/examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.nii.gz similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_echo-2_B1map.nii.gz rename to examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.nii.gz From b0138980372486b367346fb07a4ff74a5ddfe925 Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Mon, 16 Sep 2019 21:18:02 +0100 Subject: [PATCH 09/14] added details to MPM scan jsons --- .../anat/sub-01_echo-1_acq-MToff_MPM.json | 64 ++++++++++++++++++ .../anat/sub-01_echo-1_acq-MTon_MPM.json | 64 ++++++++++++++++++ .../anat/sub-01_echo-1_acq-T1w_MPM.json | 64 ++++++++++++++++++ .../anat/sub-01_echo-2_acq-MToff_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-2_acq-MTon_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-2_acq-T1w_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-3_acq-MToff_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-3_acq-MTon_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-3_acq-T1w_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-4_acq-MToff_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-4_acq-MTon_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-4_acq-T1w_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-5_acq-MToff_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-5_acq-MTon_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-5_acq-T1w_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-6_acq-MToff_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-6_acq-MTon_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-6_acq-T1w_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-7_acq-MToff_MPM.json | 65 ++++++++++++++++++- .../anat/sub-01_echo-8_acq-MToff_MPM.json | 65 ++++++++++++++++++- 20 files changed, 1280 insertions(+), 17 deletions(-) create mode 100644 examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json create mode 100644 examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json create mode 100644 examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json new file mode 100644 index 0000000..64bf467 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json @@ -0,0 +1,64 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json new file mode 100644 index 0000000..64bf467 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json @@ -0,0 +1,64 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json new file mode 100644 index 0000000..64bf467 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json @@ -0,0 +1,64 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json index 417be57..64bf467 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json @@ -1 +1,64 @@ -{"EchoTime": 0.0147} +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": "A_University_Hospital", + "InstitutionalDepartmentName": "XXXXX", + "InstitutionAddress": "Address", + "DeviceSerialNumber": "00000", + "StationName": "YYY00000", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo_MR_E11", + "MRAcquisitionType": "3D", + "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"], + "SeriesNumber": 14, + "AcquisitionTime": "13:57:54.470000", + "AcquisitionNumber": 1, + "SliceThickness": 1, + "SAR": 0.0146488, + "EchoNumber": 5, + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "PartialFourier": 1, + "BaseResolution": 256, + "ShimSetting": [ + 4942, + -11469, + -1373, + 509, + -1, + -213, + 61, + 118 ], + "TxRefAmp": 231.043, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%_mfc_3dflash", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "PercentPhaseFOV": 87.5, + "PhaseEncodingSteps": 223, + "AcquisitionMatrixPE": 224, + "ReconMatrixPE": 256, + "ParallelReductionFactorInPlane": 4, + "PixelBandwidth": 490, + "DwellTime": 4e-06, + "ImageOrientationPatientDICOM": [ + 0, + 0.866025, + -0.5, + 0, + -0.5, + -0.866025 ], + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" +} From 02016432deaa6ac3d2a1474870ab819add27dbea Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Fri, 27 Sep 2019 15:50:12 +0100 Subject: [PATCH 10/14] updated json files for MP2RAGE_singleecho --- .../mp2rage/sub-01/anat/sub-01_T1map.json | 19 ++++++++++++------- .../sub-01/anat/sub-01_inv-1_MP2RAGE.json | 7 +++++-- .../sub-01/anat/sub-01_inv-2_MP2RAGE.json | 7 +++++-- 3 files changed, 22 insertions(+), 11 deletions(-) diff --git a/examples/MP2RAGE_singleecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json b/examples/MP2RAGE_singleecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json index 2caede4..1835cac 100644 --- a/examples/MP2RAGE_singleecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json +++ b/examples/MP2RAGE_singleecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json @@ -1,9 +1,14 @@ { - "BasedOn": [ - "anat/sub-01_inv1_part-mag_MPRAGE.nii.gz", - "anat/sub-01_inv1_part-phase_MPRAGE.nii.gz", - "anat/sub-01_inv2_part-mag_MPRAGE.nii.gz", - "anat/sub-01_inv2_part-phase_MPRAGE.nii.gz" - ], - "EstimationMethod": "Marques et al., 2013" + "BasedOn": [ + "anat/sub-1_inv-1_part-mag_MP2RAGE.nii", + "anat/sub-1_inv-1_part-phase_MP2RAGE.nii", + "anat/sub-1_inv-2_part-mag_MP2RAGE.nii", + "anat/sub-1_inv-2_part-phase_MP2RAGE.nii" + ], + "EstimationReference": "Marques et al., 2010", + "EstimationAlgorithm": "MP2RAGE T1UNI", + "EstimationSoftwareName": "pymp2rage", + "EstimationSoftwareVer": "v0.1", + "EstimationSoftwareLang": "Python 3.6", + "EstimationSoftwareEnv": "Mac OS X 10.14.5" } diff --git a/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json index b1f0220..1f0cb72 100644 --- a/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json +++ b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json @@ -1,4 +1,7 @@ { - "InversionTime": 0.8, - "FlipAngle": 5 + "InversionTime": 0.8, + "FlipAngle": 5, + "ExcitationRepetitionTime": 0.0062, + "InversionRepetitionTime": 5.5, + "NumberShots": 159 } diff --git a/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json index f6cb93d..d1dfc0c 100644 --- a/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json +++ b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json @@ -1,4 +1,7 @@ { - "InversionTime": 2.7, - "FlipAngle": 7 + "InversionTime": 2.7, + "FlipAngle": 7, + "ExcitationRepetitionTime": 0.0062, + "InversionRepetitionTime": 5.5, + "NumberShots": 159 } From ce73f3e644282bf7058cc71d88cd882773c4b6eb Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Fri, 27 Sep 2019 15:57:07 +0100 Subject: [PATCH 11/14] updated json files for MP2RAGE_multiecho --- .../mp2rage/sub-01/anat/sub-01_T1map.json | 22 ++++++++++++------- .../mp2rage/sub-01/anat/sub-01_T2starmap.json | 17 ++++++++------ .../sub-01/anat/sub-01_inv-2_MP2RAGE.json | 8 ++++--- .../anat/sub-01_inv-2_echo-1_MP2RAGE.json | 7 +++++- .../anat/sub-01_inv-2_echo-2_MP2RAGE.json | 7 +++++- .../anat/sub-01_inv-2_echo-3_MP2RAGE.json | 7 +++++- .../anat/sub-01_inv-2_echo-4_MP2RAGE.json | 7 +++++- 7 files changed, 53 insertions(+), 22 deletions(-) diff --git a/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json index 54fceba..89a00dd 100644 --- a/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json +++ b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json @@ -1,10 +1,16 @@ { - "BasedOn": [ - "anat/sub-01_inv1_part-mag_MPRAGE.nii.gz", - "anat/sub-01_inv1_part-phase_MPRAGE.nii.gz", - "anat/sub-01_inv2_echo-1_part-mag_MPRAGE.nii.gz", - "anat/sub-01_inv2_echo-1_part-phase_MPRAGE.nii.gz", - "fmap/sub-01_B1map.nii.gz" - ], - "EstimationMethod": "Marques et al., 2010" + "BasedOn": [ + "anat/sub-1_inv-1_part-mag_MP2RAGE.nii", + "anat/sub-1_inv-1_part-phase_MP2RAGE.nii", + "anat/sub-1_echo-1_inv-2_part-mag_MP2RAGE.nii", + "anat/sub-1_echo-1_inv-2_part-phase_MP2RAGE.nii", + "fmap/sub-1_B1map.nii" + + ], + "EstimationReference": "Caan et al., 2019", + "EstimationAlgorithm": "MP2RAGE T1 map", + "EstimationSoftwareName": "pymp2rage", + "EstimationSoftwareVer": "v0.1", + "EstimationSoftwareLang": "Python 3.6", + "EstimationSoftwareEnv": "Mac OS X 10.14.5" } diff --git a/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.json b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.json index 3d0368d..825cf40 100644 --- a/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.json +++ b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.json @@ -1,9 +1,12 @@ { - "BasedOn": [ - "anat/sub-01_inv2_echo-1_part-mag_MPRAGE.nii.gz", - "anat/sub-01_inv2_echo-2_part-mag_MPRAGE.nii.gz", - "anat/sub-01_inv2_echo-3_part-mag_MPRAGE.nii.gz", - "anat/sub-01_inv2_echo-4_part-mag_MPRAGE.nii.gz" - ], - "EstimationMethod": "Marques et al., 2010" + "BasedOn": ["anat/sub-1_echo-1_inv-2_part-mag_MP2RAGE.nii", + "anat/sub-1_echo-2_inv-2_part-mag_MP2RAGE.nii", + "anat/sub-1_echo-3_inv-2_part-mag_MP2RAGE.nii", + "anat/sub-1_echo-4_inv-2_part-mag_MP2RAGE.nii",], + + "EstimationAlgorithm": "Ordinary Least Squares in Log-space", + "EstimationSoftwareName": "pymp2rage", + "EstimationSoftwareVer": "v0.1", + "EstimationSoftwareLang": "Python 3.6", + "EstimationSoftwareEnv": "Mac OS X 10.14.5" } diff --git a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json index 18a74e4..fc09871 100644 --- a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json @@ -1,5 +1,7 @@ { - "InversionTime": 3.855, - "FlipAngle": 6, - "RepetitionTimeExcitation": 0.032 + "InversionTime": 0.67, + "FlipAngle": 7, + "ExcitationRepetitionTime": 0.0062, + "InversionRepetitionTime": 6.723, + "NumberShots": 150 } diff --git a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_MP2RAGE.json b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_MP2RAGE.json index 6e56745..9afc5d8 100644 --- a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_MP2RAGE.json +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_MP2RAGE.json @@ -1,3 +1,8 @@ { - "EchoTime": 0.006 + "InversionTime": 3.855, + "FlipAngle": 6, + "ExcitationRepetitionTime": 0.032, + "InversionRepetitionTime": 6.723, + "NumberShots": 150, + "EchoTime": 0.006 } diff --git a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_MP2RAGE.json b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_MP2RAGE.json index d257a48..195dd74 100644 --- a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_MP2RAGE.json +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_MP2RAGE.json @@ -1,3 +1,8 @@ { - "EchoTime": 0.0145 + "InversionTime": 3.855, + "FlipAngle": 6, + "ExcitationRepetitionTime": 0.032, + "InversionRepetitionTime": 6.723, + "NumberShots": 150, + "EchoTime": 0.0145 } diff --git a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_MP2RAGE.json b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_MP2RAGE.json index 878ae21..c03d18a 100644 --- a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_MP2RAGE.json +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_MP2RAGE.json @@ -1,3 +1,8 @@ { - "EchoTime": 0.023 + "InversionTime": 3.855, + "FlipAngle": 6, + "ExcitationRepetitionTime": 0.032, + "InversionRepetitionTime": 6.723, + "NumberShots": 150, + "EchoTime": 0.0230 } diff --git a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_MP2RAGE.json b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_MP2RAGE.json index 92a848f..9370aae 100644 --- a/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_MP2RAGE.json +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_MP2RAGE.json @@ -1,3 +1,8 @@ { - "EchoTime": 0.0315 + "InversionTime": 3.855, + "FlipAngle": 6, + "ExcitationRepetitionTime": 0.032, + "InversionRepetitionTime": 6.723, + "NumberShots": 150, + "EchoTime": 0.0315 } From c4d09cfcfbd3e073109f310a317d19073a490d4e Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Fri, 27 Sep 2019 16:12:20 +0100 Subject: [PATCH 12/14] updated jsons for MPM fieldmaps --- .../hmri/sub-01/fmap/sub-01_B0map.json | 2 +- .../hmri/sub-01/fmap/sub-01_B1plusmap.json | 2 +- .../sub-01/fmap/sub-01_B1minusmap_MToff.json | 10 ++++++++ ....nii.gz => sub-01_B1minusmap_MToff.nii.gz} | Bin .../sub-01/fmap/sub-01_B1minusmap_MTon.json | 8 +++++++ ...w.nii.gz => sub-01_B1minusmap_MTon.nii.gz} | Bin .../sub-01/fmap/sub-01_B1minusmap_MTw.json | 8 ------- .../sub-01/fmap/sub-01_B1minusmap_PDw.json | 10 -------- .../sub-01/fmap/sub-01_B1minusmap_T1w.json | 12 +++++----- .../sub-01/fmap/sub-01_echo-1_B1plusmap.json | 22 +++++++++++++++++- .../fmap/sub-01_echo-1_part-mag_B0map.json | 22 +++++++++++++++++- .../sub-01/fmap/sub-01_echo-2_B1plusmap.json | 22 +++++++++++++++++- .../fmap/sub-01_echo-2_part-mag_B0map.json | 22 +++++++++++++++++- .../fmap/sub-01_echo-2_part-phase_B0map.json | 21 +++++++++++++++++ 14 files changed, 131 insertions(+), 30 deletions(-) create mode 100644 examples/MPM/sub-01/fmap/sub-01_B1minusmap_MToff.json rename examples/MPM/sub-01/fmap/{sub-01_B1minusmap_MTw.nii.gz => sub-01_B1minusmap_MToff.nii.gz} (100%) create mode 100644 examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTon.json rename examples/MPM/sub-01/fmap/{sub-01_B1minusmap_PDw.nii.gz => sub-01_B1minusmap_MTon.nii.gz} (100%) delete mode 100644 examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.json delete mode 100644 examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.json diff --git a/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.json b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.json index ed26345..83aa41a 100644 --- a/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.json +++ b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.json @@ -1,5 +1,5 @@ {"IntendedFor": ["anat/sub-01_PDmap.nii.gz", - "anat/sub-01_MTmap.nii.gz", + "anat/sub-01_MTsat.nii.gz", "anat/sub-01_R1map.nii.gz", "anat/sub-01_R2starmap.nii.gz"], "RepetitionTime": 1.02, diff --git a/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.json b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.json index 34faae0..bd20163 100644 --- a/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.json +++ b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.json @@ -1,4 +1,4 @@ {"IntendedFor": ["anat/sub-01_PDmap.nii.gz", - "anat/sub-01_MTmap.nii.gz", + "anat/sub-01_MTsat.nii.gz", "anat/sub-01_R1map.nii.gz", "anat/sub-01_R2starmap.nii.gz"]} diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MToff.json b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MToff.json new file mode 100644 index 0000000..49dcbe2 --- /dev/null +++ b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MToff.json @@ -0,0 +1,10 @@ +{"IntendedFor":["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz"] + +} diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.nii.gz b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MToff.nii.gz similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.nii.gz rename to examples/MPM/sub-01/fmap/sub-01_B1minusmap_MToff.nii.gz diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTon.json b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTon.json new file mode 100644 index 0000000..7322117 --- /dev/null +++ b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTon.json @@ -0,0 +1,8 @@ +{"IntendedFor":["anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz"] + +} diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.nii.gz b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTon.nii.gz similarity index 100% rename from examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.nii.gz rename to examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTon.nii.gz diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.json b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.json deleted file mode 100644 index f89017c..0000000 --- a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_MTw.json +++ /dev/null @@ -1,8 +0,0 @@ -{"IntendedFor":["anat/sub-01_echo-1_part-mag_MTw.nii.gz", - "anat/sub-01_echo-2_part-mag_MTw.nii.gz", - "anat/sub-01_echo-3_part-mag_MTw.nii.gz", - "anat/sub-01_echo-4_part-mag_MTw.nii.gz", - "anat/sub-01_echo-5_part-mag_MTw.nii.gz", - "anat/sub-01_echo-6_part-mag_MTw.nii.gz"] - -} diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.json b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.json deleted file mode 100644 index bb8d9dc..0000000 --- a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_PDw.json +++ /dev/null @@ -1,10 +0,0 @@ -{"IntendedFor":["anat/sub-01_echo-1_part-mag_PDw.nii.gz", - "anat/sub-01_echo-2_part-mag_PDw.nii.gz", - "anat/sub-01_echo-3_part-mag_PDw.nii.gz", - "anat/sub-01_echo-4_part-mag_PDw.nii.gz", - "anat/sub-01_echo-5_part-mag_PDw.nii.gz", - "anat/sub-01_echo-6_part-mag_PDw.nii.gz", - "anat/sub-01_echo-7_part-mag_PDw.nii.gz", - "anat/sub-01_echo-8_part-mag_PDw.nii.gz"] - -} diff --git a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.json b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.json index 9542f67..45fd687 100644 --- a/examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.json +++ b/examples/MPM/sub-01/fmap/sub-01_B1minusmap_T1w.json @@ -1,7 +1,7 @@ -{"IntendedFor":["anat/sub-01_echo-1_part-mag_T1w.nii.gz", - "anat/sub-01_echo-2_part-mag_T1w.nii.gz", - "anat/sub-01_echo-3_part-mag_T1w.nii.gz", - "anat/sub-01_echo-4_part-mag_T1w.nii.gz", - "anat/sub-01_echo-5_part-mag_T1w.nii.gz", - "anat/sub-01_echo-6_part-mag_T1w.nii.gz"] +{"IntendedFor":["anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz"] } diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-1_B1plusmap.json b/examples/MPM/sub-01/fmap/sub-01_echo-1_B1plusmap.json index 1b3b43c..d90e38c 100644 --- a/examples/MPM/sub-01/fmap/sub-01_echo-1_B1plusmap.json +++ b/examples/MPM/sub-01/fmap/sub-01_echo-1_B1plusmap.json @@ -1 +1,21 @@ -{"EchoTime”: 0.03706} +{ "IntendedFor":["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz"] +} diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-1_part-mag_B0map.json b/examples/MPM/sub-01/fmap/sub-01_echo-1_part-mag_B0map.json index 9561d0b..d90e38c 100644 --- a/examples/MPM/sub-01/fmap/sub-01_echo-1_part-mag_B0map.json +++ b/examples/MPM/sub-01/fmap/sub-01_echo-1_part-mag_B0map.json @@ -1 +1,21 @@ -{"EchoTime": 0.01} +{ "IntendedFor":["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz"] +} diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.json b/examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.json index b7d1e8d..d90e38c 100644 --- a/examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.json +++ b/examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.json @@ -1 +1,21 @@ -{"EchoTime”: 0.01853} +{ "IntendedFor":["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz"] +} diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json index 6546cbd..d90e38c 100644 --- a/examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json +++ b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json @@ -1 +1,21 @@ -{"EchoTime": 0.01246} +{ "IntendedFor":["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz"] +} diff --git a/examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json index e69de29..d90e38c 100644 --- a/examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json +++ b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.json @@ -0,0 +1,21 @@ +{ "IntendedFor":["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz"] +} From 9183c89c1748799e1d37e9fba418de53e23130e2 Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Fri, 27 Sep 2019 16:36:00 +0100 Subject: [PATCH 13/14] created realistic json for MPM echoes --- .../hmri/sub-01/anat/sub-01_MTsat.json | 68 +++++++++++------- .../hmri/sub-01/anat/sub-01_PDmap.json | 69 ++++++++++++------- .../hmri/sub-01/anat/sub-01_R1map.json | 69 ++++++++++++------- .../hmri/sub-01/anat/sub-01_R2starmap.json | 69 ++++++++++++------- .../anat/sub-01_echo-1_acq-MToff_MPM.json | 9 ++- .../anat/sub-01_echo-1_acq-MTon_MPM.json | 13 ++-- .../anat/sub-01_echo-1_acq-T1w_MPM.json | 13 ++-- .../anat/sub-01_echo-2_acq-MToff_MPM.json | 9 ++- .../anat/sub-01_echo-2_acq-MTon_MPM.json | 13 ++-- .../anat/sub-01_echo-2_acq-T1w_MPM.json | 13 ++-- .../anat/sub-01_echo-3_acq-MToff_MPM.json | 9 ++- .../anat/sub-01_echo-3_acq-MTon_MPM.json | 13 ++-- .../anat/sub-01_echo-3_acq-T1w_MPM.json | 13 ++-- .../anat/sub-01_echo-4_acq-MToff_MPM.json | 9 ++- .../anat/sub-01_echo-4_acq-MTon_MPM.json | 13 ++-- .../anat/sub-01_echo-4_acq-T1w_MPM.json | 13 ++-- .../anat/sub-01_echo-5_acq-MToff_MPM.json | 9 ++- .../anat/sub-01_echo-5_acq-MTon_MPM.json | 13 ++-- .../anat/sub-01_echo-5_acq-T1w_MPM.json | 13 ++-- .../anat/sub-01_echo-6_acq-MToff_MPM.json | 9 ++- .../anat/sub-01_echo-6_acq-MTon_MPM.json | 13 ++-- .../anat/sub-01_echo-6_acq-T1w_MPM.json | 13 ++-- .../anat/sub-01_echo-7_acq-MToff_MPM.json | 9 ++- .../anat/sub-01_echo-8_acq-MToff_MPM.json | 9 ++- 24 files changed, 276 insertions(+), 227 deletions(-) diff --git a/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_MTsat.json b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_MTsat.json index 3529b6b..ad84b76 100644 --- a/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_MTsat.json +++ b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_MTsat.json @@ -1,25 +1,43 @@ -{"BasedOn": ["fmap/sub-01_echo-1_B1map.nii.gz", - "fmap/sub-01_echo-2_B1map.nii.gz", - "fmap/sub-01_echo-1_part-mag_B0map.nii.gz", - "fmap/sub-01_echo-2_part-mag_B0map.nii.gz", - "anat/sub-01_echo-1_part-mag_MTw.nii.gz", - "anat/sub-01_echo-2_part-mag_MTw.nii.gz", - "anat/sub-01_echo-3_part-mag_MTw.nii.gz", - "anat/sub-01_echo-4_part-mag_MTw.nii.gz", - "anat/sub-01_echo-5_part-mag_MTw.nii.gz", - "anat/sub-01_echo-6_part-mag_MTw.nii.gz", - "anat/sub-01_echo-1_part-mag_PDw.nii.gz", - "anat/sub-01_echo-2_part-mag_PDw.nii.gz", - "anat/sub-01_echo-3_part-mag_PDw.nii.gz", - "anat/sub-01_echo-4_part-mag_PDw.nii.gz", - "anat/sub-01_echo-5_part-mag_PDw.nii.gz", - "anat/sub-01_echo-6_part-mag_PDw.nii.gz", - "anat/sub-01_echo-7_part-mag_PDw.nii.gz", - "anat/sub-01_echo-8_part-mag_PDw.nii.gz", - "anat/sub-01_echo-1_part-mag_T1w.nii.gz", - "anat/sub-01_echo-2_part-mag_T1w.nii.gz", - "anat/sub-01_echo-3_part-mag_T1w.nii.gz", - "anat/sub-01_echo-4_part-mag_T1w.nii.gz", - "anat/sub-01_echo-5_part-mag_T1w.nii.gz", - "anat/sub-01_echo-6_part-mag_T1w.nii.gz"], -"EstimationMethod": "Weiskopf et al, 2013"} +{"BasedOn": ["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz", + "fmap/sub-01_B1minusmap_MTon.json", + "fmap/sub-01_B1minusmap_MToff.json", + "fmap/sub-01_B1minusmap_T1w.json", + "fmap/sub-01_echo-1_B1plusmap.json", + "fmap/sub-01_echo-1_part-mag_B0map.json", + "fmap/sub-01_echo-2_B1plusmap.json", + "fmap/sub-01_echo-2_part-phase_B0map.json", + "fmap/sub-01_echo-2_part-mag_B0map.json"] + "MagneticFieldStrength": "3", + "Manufacturer": "Siemens", + "ManufacturerModelName": "Prisma", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + “SequenceName": "fl3d_1i3d8", + "RepetitionTime": "0.025", + "FlipAngle": ["6","21"], + "EstimationPaper":"Tabelow et al., 2019, Neuroimage", + "EstimationAlgorithm":"Ernst equation", + "EstimationSoftwareName": "SPM hMRI", + "EstimationSoftwareLanguage": "MATLAB", + "EstimationSoftwareVersion": "0.2.0", + "EstimationSoftwareEnv": "OSX 10.14" +} diff --git a/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_PDmap.json b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_PDmap.json index 7370b6c..ad84b76 100644 --- a/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_PDmap.json +++ b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_PDmap.json @@ -1,26 +1,43 @@ -{"BasedOn": ["fmap/sub-01_echo-1_B1map.nii.gz", - "fmap/sub-01_echo-2_B1map.nii.gz", - "fmap/sub-01_echo-1_part-mag_B0map.nii.gz", - "fmap/sub-01_echo-2_part-mag_B0map.nii.gz", - "fmap/sub-01_echo-2_part-phase_B0map.nii.gz", - "anat/sub-01_echo-1_part-mag_MTw.nii.gz", - "anat/sub-01_echo-2_part-mag_MTw.nii.gz", - "anat/sub-01_echo-3_part-mag_MTw.nii.gz", - "anat/sub-01_echo-4_part-mag_MTw.nii.gz", - "anat/sub-01_echo-5_part-mag_MTw.nii.gz", - "anat/sub-01_echo-6_part-mag_MTw.nii.gz", - "anat/sub-01_echo-1_part-mag_PDw.nii.gz", - "anat/sub-01_echo-2_part-mag_PDw.nii.gz", - "anat/sub-01_echo-3_part-mag_PDw.nii.gz", - "anat/sub-01_echo-4_part-mag_PDw.nii.gz", - "anat/sub-01_echo-5_part-mag_PDw.nii.gz", - "anat/sub-01_echo-6_part-mag_PDw.nii.gz", - "anat/sub-01_echo-7_part-mag_PDw.nii.gz", - "anat/sub-01_echo-8_part-mag_PDw.nii.gz", - "anat/sub-01_echo-1_part-mag_T1w.nii.gz", - "anat/sub-01_echo-2_part-mag_T1w.nii.gz", - "anat/sub-01_echo-3_part-mag_T1w.nii.gz", - "anat/sub-01_echo-4_part-mag_T1w.nii.gz", - "anat/sub-01_echo-5_part-mag_T1w.nii.gz", - "anat/sub-01_echo-6_part-mag_T1w.nii.gz"], -"EstimationMethod": "Weiskopf et al, 2013"} +{"BasedOn": ["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz", + "fmap/sub-01_B1minusmap_MTon.json", + "fmap/sub-01_B1minusmap_MToff.json", + "fmap/sub-01_B1minusmap_T1w.json", + "fmap/sub-01_echo-1_B1plusmap.json", + "fmap/sub-01_echo-1_part-mag_B0map.json", + "fmap/sub-01_echo-2_B1plusmap.json", + "fmap/sub-01_echo-2_part-phase_B0map.json", + "fmap/sub-01_echo-2_part-mag_B0map.json"] + "MagneticFieldStrength": "3", + "Manufacturer": "Siemens", + "ManufacturerModelName": "Prisma", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + “SequenceName": "fl3d_1i3d8", + "RepetitionTime": "0.025", + "FlipAngle": ["6","21"], + "EstimationPaper":"Tabelow et al., 2019, Neuroimage", + "EstimationAlgorithm":"Ernst equation", + "EstimationSoftwareName": "SPM hMRI", + "EstimationSoftwareLanguage": "MATLAB", + "EstimationSoftwareVersion": "0.2.0", + "EstimationSoftwareEnv": "OSX 10.14" +} diff --git a/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R1map.json b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R1map.json index 204d07c..ad84b76 100644 --- a/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R1map.json +++ b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R1map.json @@ -1,26 +1,43 @@ -{"BasedOn": ["fmap/sub-01_echo-1_B1map.nii.gz", - "fmap/sub-01_echo-2_B1map.nii.gz", - "fmap/sub-01_echo-1_part-mag_B0map.nii.gz", - "fmap/sub-01_echo-2_part-mag_B0map.nii.gz", - "fmap/sub-01_echo-2_part-phase_B0map.nii.gz", - "anat/sub-01_echo-1_part-mag_MTw.nii.gz", - "anat/sub-01_echo-2_part-mag_MTw.nii.gz", - "anat/sub-01_echo-3_part-mag_MTw.nii.gz", - "anat/sub-01_echo-4_part-mag_MTw.nii.gz", - "anat/sub-01_echo-5_part-mag_MTw.nii.gz", - "anat/sub-01_echo-6_part-mag_MTw.nii.gz", - "anat/sub-01_echo-1_part-mag_PDw.nii.gz", - "anat/sub-01_echo-2_part-mag_PDw.nii.gz", - "anat/sub-01_echo-3_part-mag_PDw.nii.gz", - "anat/sub-01_echo-4_part-mag_PDw.nii.gz", - "anat/sub-01_echo-5_part-mag_PDw.nii.gz", - "anat/sub-01_echo-6_part-mag_PDw.nii.gz", - "anat/sub-01_echo-7_part-mag_PDw.nii.gz", - "anat/sub-01_echo-8_part-mag_PDw.nii.gz", - "anat/sub-01_echo-1_part-mag_T1w.nii.gz", - "anat/sub-01_echo-2_part-mag_T1w.nii.gz", - "anat/sub-01_echo-3_part-mag_T1w.nii.gz", - "anat/sub-01_echo-4_part-mag_T1w.nii.gz", - "anat/sub-01_echo-5_part-mag_T1w.nii.gz", - "anat/sub-01_echo-6_part-mag_T1w.nii.gz"], -"EstimationMethod": "Weiskopf et al, 2013"} +{"BasedOn": ["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz", + "fmap/sub-01_B1minusmap_MTon.json", + "fmap/sub-01_B1minusmap_MToff.json", + "fmap/sub-01_B1minusmap_T1w.json", + "fmap/sub-01_echo-1_B1plusmap.json", + "fmap/sub-01_echo-1_part-mag_B0map.json", + "fmap/sub-01_echo-2_B1plusmap.json", + "fmap/sub-01_echo-2_part-phase_B0map.json", + "fmap/sub-01_echo-2_part-mag_B0map.json"] + "MagneticFieldStrength": "3", + "Manufacturer": "Siemens", + "ManufacturerModelName": "Prisma", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + “SequenceName": "fl3d_1i3d8", + "RepetitionTime": "0.025", + "FlipAngle": ["6","21"], + "EstimationPaper":"Tabelow et al., 2019, Neuroimage", + "EstimationAlgorithm":"Ernst equation", + "EstimationSoftwareName": "SPM hMRI", + "EstimationSoftwareLanguage": "MATLAB", + "EstimationSoftwareVersion": "0.2.0", + "EstimationSoftwareEnv": "OSX 10.14" +} diff --git a/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R2starmap.json b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R2starmap.json index 54013c8..ad84b76 100644 --- a/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R2starmap.json +++ b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R2starmap.json @@ -1,26 +1,43 @@ -{"BasedOn": ["fmap/sub-01_echo-1_B1map.nii.gz", - "fmap/sub-01_echo-2_B1map.nii.gz", - "fmap/sub-01_echo-1_part-mag_B0map.nii.gz", - "fmap/sub-01_echo-2_part-mag_B0map.nii.gz", - "anat/sub-01_echo-1_part-mag_MTw.nii.gz", - "anat/sub-01_echo-2_part-mag_MTw.nii.gz", - "anat/sub-01_echo-3_part-mag_MTw.nii.gz", - "anat/sub-01_echo-4_part-mag_MTw.nii.gz", - "anat/sub-01_echo-5_part-mag_MTw.nii.gz", - "anat/sub-01_echo-6_part-mag_MTw.nii.gz", - "anat/sub-01_echo-1_part-mag_PDw.nii.gz", - "anat/sub-01_echo-2_part-mag_PDw.nii.gz", - "anat/sub-01_echo-3_part-mag_PDw.nii.gz", - "anat/sub-01_echo-4_part-mag_PDw.nii.gz", - "anat/sub-01_echo-5_part-mag_PDw.nii.gz", - "anat/sub-01_echo-6_part-mag_PDw.nii.gz", - "anat/sub-01_echo-7_part-mag_PDw.nii.gz", - "anat/sub-01_echo-8_part-mag_PDw.nii.gz", - "anat/sub-01_echo-1_part-mag_T1w.nii.gz", - "anat/sub-01_echo-2_part-mag_T1w.nii.gz", - "anat/sub-01_echo-3_part-mag_T1w.nii.gz", - "anat/sub-01_echo-4_part-mag_T1w.nii.gz", - "anat/sub-01_echo-5_part-mag_T1w.nii.gz", - "anat/sub-01_echo-6_part-mag_T1w.nii.gz"], -"EstimationMethod": "Weiskopf et al, 2013"} - +{"BasedOn": ["anat/sub-01_echo-1_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-8_part-mag_acq-MToff_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-MTon_MPM.nii.gz", + "anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-4_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-5_part-mag_acq-T1w_MPM.nii.gz", + "anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz", + "fmap/sub-01_B1minusmap_MTon.json", + "fmap/sub-01_B1minusmap_MToff.json", + "fmap/sub-01_B1minusmap_T1w.json", + "fmap/sub-01_echo-1_B1plusmap.json", + "fmap/sub-01_echo-1_part-mag_B0map.json", + "fmap/sub-01_echo-2_B1plusmap.json", + "fmap/sub-01_echo-2_part-phase_B0map.json", + "fmap/sub-01_echo-2_part-mag_B0map.json"] + "MagneticFieldStrength": "3", + "Manufacturer": "Siemens", + "ManufacturerModelName": "Prisma", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + “SequenceName": "fl3d_1i3d8", + "RepetitionTime": "0.025", + "FlipAngle": ["6","21"], + "EstimationPaper":"Tabelow et al., 2019, Neuroimage", + "EstimationAlgorithm":"Ernst equation", + "EstimationSoftwareName": "SPM hMRI", + "EstimationSoftwareLanguage": "MATLAB", + "EstimationSoftwareVersion": "0.2.0", + "EstimationSoftwareEnv": "OSX 10.14" +} diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json index 64bf467..fa97178 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0023, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json index 64bf467..da18d6b 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0023, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json index 64bf467..d895526 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0023, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json index 64bf467..f374474 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0046, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json index 64bf467..c3bf822 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0046, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json index 64bf467..3509c4d 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0046, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json index 64bf467..00aca3b 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0069, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json index 64bf467..cff35fa 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0069, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json index 64bf467..1da6a93 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0069, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json index 64bf467..87f996e 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0092, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json index 64bf467..443676b 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0092, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json index 64bf467..87c7583 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0092, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json index 64bf467..caec479 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json index 64bf467..e91e833 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json index 64bf467..3417069 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json index 64bf467..4525e0c 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0138, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json index 64bf467..7ce383c 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0138, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json index 64bf467..3b1e03a 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0138, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -12,8 +16,8 @@ "PatientPosition": "HFS", "SoftwareVersions": "syngo_MR_E11", "MRAcquisitionType": "3D", - "SeriesDescription": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", - "ProtocolName": "mfc_3dflash_PDw_GRAPPA4_PSN_488BW", + "SeriesDescription": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", "ScanningSequence": "RM", "SequenceVariant": "SP", "SequenceName": "fl3d_1i3d8", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json index 64bf467..053edd1 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0161, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } diff --git a/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json index 64bf467..f201e0e 100644 --- a/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json +++ b/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json @@ -1,4 +1,8 @@ { + "EchoTime": 0.0184, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", "Modality": "MR", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -24,9 +28,6 @@ "SliceThickness": 1, "SAR": 0.0146488, "EchoNumber": 5, - "EchoTime": 0.0115, - "RepetitionTime": 0.025, - "FlipAngle": 6, "PartialFourier": 1, "BaseResolution": 256, "ShimSetting": [ @@ -59,6 +60,4 @@ -0.5, -0.866025 ], "InPlanePhaseEncodingDirectionDICOM": "ROW", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20180325 GCC4.8.5" } From 9f83abdfc9c23fa6b8ef13dd3ac43ddcbaab6488 Mon Sep 17 00:00:00 2001 From: Alberto Lazari Date: Fri, 27 Sep 2019 16:42:49 +0100 Subject: [PATCH 14/14] MEGRE json expansion --- .../derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json | 4 ++-- .../qsm_pipeline/sub-01/anat/sub-01_T2starmap.json | 6 +++--- .../MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json | 8 +++++++- .../MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json | 8 +++++++- .../MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json | 8 +++++++- 5 files changed, 26 insertions(+), 8 deletions(-) diff --git a/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json index bda495c..bf13ce5 100644 --- a/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json +++ b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json @@ -1,7 +1,7 @@ { "BasedOn": [ - "anat/sub-01_echo-1_part-mag_FLASH.nii.gz", - "anat/sub-01_echo-1_part-phase_FLASH.nii.gz" + "anat/sub-01_echo-1_part-mag_MEGRE.nii.gz", + "anat/sub-01_echo-1_part-phase_MEGRE.nii.gz" ], "EstimationMethod": "Schaefer et al., 2011" } diff --git a/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json index b159cd0..857b976 100644 --- a/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json +++ b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json @@ -1,8 +1,8 @@ { "BasedOn": [ - "anat/sub-01_echo-1_part-mag_FLASH.nii.gz", - "anat/sub-01_echo-2_part-mag_FLASH.nii.gz", - "anat/sub-01_echo-3_part-mag_FLASH.nii.gz" + "anat/sub-01_echo-1_part-mag_MEGRE.nii.gz", + "anat/sub-01_echo-2_part-mag_MEGRE.nii.gz", + "anat/sub-01_echo-3_part-mag_MEGRE.nii.gz" ], "EstimationMethod": "Linear least-squares" } diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json index 755f482..7e7ffdf 100644 --- a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json +++ b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json @@ -1,3 +1,9 @@ { - "EchoTime": 0.01 + "IntendedFor": ["anat/sub-01_T2starmap.nii.gz", + "anat/sub-01_QSM.nii.gz"], + "MagneticFieldStrength": "3", + "Manufacturer": "GE", + "PulseSequenceType": "SPGR", + "RepetitionTime": "0.0150", + "FlipAngle": "3" } diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json index 3d2e5b4..7e7ffdf 100644 --- a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json +++ b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json @@ -1,3 +1,9 @@ { - "EchoTime": 0.02 + "IntendedFor": ["anat/sub-01_T2starmap.nii.gz", + "anat/sub-01_QSM.nii.gz"], + "MagneticFieldStrength": "3", + "Manufacturer": "GE", + "PulseSequenceType": "SPGR", + "RepetitionTime": "0.0150", + "FlipAngle": "3" } diff --git a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json index 6928485..7e7ffdf 100644 --- a/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json +++ b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json @@ -1,3 +1,9 @@ { - "EchoTime": 0.03 + "IntendedFor": ["anat/sub-01_T2starmap.nii.gz", + "anat/sub-01_QSM.nii.gz"], + "MagneticFieldStrength": "3", + "Manufacturer": "GE", + "PulseSequenceType": "SPGR", + "RepetitionTime": "0.0150", + "FlipAngle": "3" }