diff --git a/examples/BEP001_examples.md b/examples/BEP001_examples.md new file mode 100644 index 0000000..75d1410 --- /dev/null +++ b/examples/BEP001_examples.md @@ -0,0 +1,22 @@ +# BEP001 examples + +This branch of the BEP001 repository contains some practical examples of what a BIDS-compatible qMRI dataset will look like. + +You can find more about the BEP001 addition to the BIDS standard, and the rationale for the 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. +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. 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/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 new file mode 100644 index 0000000..bf13ce5 --- /dev/null +++ b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json @@ -0,0 +1,7 @@ +{ + "BasedOn": [ + "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/ds-01/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/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/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 new file mode 100644 index 0000000..857b976 --- /dev/null +++ b/examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json @@ -0,0 +1,8 @@ +{ + "BasedOn": [ + "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/ds-03/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-03/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/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json new file mode 100644 index 0000000..7e7ffdf --- /dev/null +++ b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json @@ -0,0 +1,9 @@ +{ + "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/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/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_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json new file mode 100644 index 0000000..7e7ffdf --- /dev/null +++ b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json @@ -0,0 +1,9 @@ +{ + "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/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/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_MEGRE.json b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json new file mode 100644 index 0000000..7e7ffdf --- /dev/null +++ b/examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json @@ -0,0 +1,9 @@ +{ + "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/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/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/ds-03/dataset_description.json b/examples/MP2RAGE_multiecho/dataset_description.json similarity index 100% rename from examples/ds-03/dataset_description.json rename to examples/MP2RAGE_multiecho/dataset_description.json 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 new file mode 100644 index 0000000..89a00dd --- /dev/null +++ b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json @@ -0,0 +1,16 @@ +{ + "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/ds-02/sub-01/anat/sub-01_T1map.nii.gz b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.nii.gz similarity index 100% rename from examples/ds-02/sub-01/anat/sub-01_T1map.nii.gz rename to examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.nii.gz 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 new file mode 100644 index 0000000..825cf40 --- /dev/null +++ b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.json @@ -0,0 +1,12 @@ +{ + "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/ds-02/sub-01/anat/sub-01_T1w.nii.gz b/examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.nii.gz similarity index 100% rename from examples/ds-02/sub-01/anat/sub-01_T1w.nii.gz rename to examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.nii.gz diff --git a/examples/ds-03/sub-01/anat/sub-01_T1w.json b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_T1w.json similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_T1w.json rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_T1w.json diff --git a/examples/ds-03/sub-01/anat/sub-01_T1w.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_T1w.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_T1w.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_T1w.nii.gz diff --git a/examples/ds-02/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-02/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz diff --git a/examples/ds-02/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-02/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz 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 new file mode 100644 index 0000000..fc09871 --- /dev/null +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json @@ -0,0 +1,7 @@ +{ + "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 new file mode 100644 index 0000000..9afc5d8 --- /dev/null +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_MP2RAGE.json @@ -0,0 +1,8 @@ +{ + "InversionTime": 3.855, + "FlipAngle": 6, + "ExcitationRepetitionTime": 0.032, + "InversionRepetitionTime": 6.723, + "NumberShots": 150, + "EchoTime": 0.006 +} diff --git a/examples/ds-02/sub-01/anat/sub-01_inv-2_part-mag_MP2RAGE.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_part-mag_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-02/sub-01/anat/sub-01_inv-2_part-mag_MP2RAGE.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_part-mag_MP2RAGE.nii.gz diff --git a/examples/ds-02/sub-01/anat/sub-01_inv-2_part-phase_MP2RAGE.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_part-phase_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-02/sub-01/anat/sub-01_inv-2_part-phase_MP2RAGE.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_part-phase_MP2RAGE.nii.gz 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 new file mode 100644 index 0000000..195dd74 --- /dev/null +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_MP2RAGE.json @@ -0,0 +1,8 @@ +{ + "InversionTime": 3.855, + "FlipAngle": 6, + "ExcitationRepetitionTime": 0.032, + "InversionRepetitionTime": 6.723, + "NumberShots": 150, + "EchoTime": 0.0145 +} diff --git a/examples/ds-03/sub-01/anat/json.tool b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_part-mag_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/json.tool rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_part-mag_MP2RAGE.nii.gz diff --git a/examples/ds-03/sub-01/anat/sub-01_T1map.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_part-phase_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_T1map.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_part-phase_MP2RAGE.nii.gz 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 new file mode 100644 index 0000000..c03d18a --- /dev/null +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_MP2RAGE.json @@ -0,0 +1,8 @@ +{ + "InversionTime": 3.855, + "FlipAngle": 6, + "ExcitationRepetitionTime": 0.032, + "InversionRepetitionTime": 6.723, + "NumberShots": 150, + "EchoTime": 0.0230 +} diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-mag_MP2RAGE.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_part-mag_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-mag_MP2RAGE.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_part-mag_MP2RAGE.nii.gz diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-phase_MP2RAGE.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_part-phase_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_echo-1_inv-2_part-phase_MP2RAGE.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_part-phase_MP2RAGE.nii.gz 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 new file mode 100644 index 0000000..9370aae --- /dev/null +++ b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_MP2RAGE.json @@ -0,0 +1,8 @@ +{ + "InversionTime": 3.855, + "FlipAngle": 6, + "ExcitationRepetitionTime": 0.032, + "InversionRepetitionTime": 6.723, + "NumberShots": 150, + "EchoTime": 0.0315 +} diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-mag_MP2RAGE.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_part-mag_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-mag_MP2RAGE.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_part-mag_MP2RAGE.nii.gz diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-phase_MP2RAGE.nii.gz b/examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_part-phase_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_echo-2_inv-2_part-phase_MP2RAGE.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_part-phase_MP2RAGE.nii.gz diff --git a/examples/ds-03/sub-01/fmap/sub-01_B1map.json b/examples/MP2RAGE_multiecho/sub-01/fmap/sub-01_B1map.json similarity index 100% rename from examples/ds-03/sub-01/fmap/sub-01_B1map.json rename to examples/MP2RAGE_multiecho/sub-01/fmap/sub-01_B1map.json diff --git a/examples/ds-03/sub-01/fmap/sub-01_B1map.nii.gz b/examples/MP2RAGE_multiecho/sub-01/fmap/sub-01_B1map.nii.gz similarity index 100% rename from examples/ds-03/sub-01/fmap/sub-01_B1map.nii.gz rename to examples/MP2RAGE_multiecho/sub-01/fmap/sub-01_B1map.nii.gz diff --git a/examples/ds-02/dataset_description.json b/examples/MP2RAGE_singleecho/dataset_description.json similarity index 100% rename from examples/ds-02/dataset_description.json rename to examples/MP2RAGE_singleecho/dataset_description.json 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 new file mode 100644 index 0000000..1835cac --- /dev/null +++ b/examples/MP2RAGE_singleecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json @@ -0,0 +1,14 @@ +{ + "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/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-mag_MP2RAGE.nii.gz b/examples/MP2RAGE_singleecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-mag_MP2RAGE.nii.gz rename to examples/MP2RAGE_singleecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.nii.gz diff --git a/examples/ds-02/sub-01/anat/sub-01_T1w.json b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_T1w.json similarity index 100% rename from examples/ds-02/sub-01/anat/sub-01_T1w.json rename to examples/MP2RAGE_singleecho/sub-01/anat/sub-01_T1w.json diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-phase_MP2RAGE.nii.gz b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_T1w.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_echo-3_inv-2_part-phase_MP2RAGE.nii.gz rename to examples/MP2RAGE_singleecho/sub-01/anat/sub-01_T1w.nii.gz 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 new file mode 100644 index 0000000..1f0cb72 --- /dev/null +++ b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json @@ -0,0 +1,7 @@ +{ + "InversionTime": 0.8, + "FlipAngle": 5, + "ExcitationRepetitionTime": 0.0062, + "InversionRepetitionTime": 5.5, + "NumberShots": 159 +} diff --git a/examples/ds-03/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz rename to examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz diff --git a/examples/ds-03/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz rename to examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_part-phase_MP2RAGE.nii.gz 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 new file mode 100644 index 0000000..d1dfc0c --- /dev/null +++ b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json @@ -0,0 +1,7 @@ +{ + "InversionTime": 2.7, + "FlipAngle": 7, + "ExcitationRepetitionTime": 0.0062, + "InversionRepetitionTime": 5.5, + "NumberShots": 159 +} diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-mag_MP2RAGE.nii.gz b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_part-mag_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-mag_MP2RAGE.nii.gz rename to examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_part-mag_MP2RAGE.nii.gz diff --git a/examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-phase_MP2RAGE.nii.gz b/examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_part-phase_MP2RAGE.nii.gz similarity index 100% rename from examples/ds-03/sub-01/anat/sub-01_echo-4_inv-2_part-phase_MP2RAGE.nii.gz rename to examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_part-phase_MP2RAGE.nii.gz diff --git a/examples/ds-04/dataset_description.json b/examples/MPM/dataset_description.json similarity index 100% rename from examples/ds-04/dataset_description.json rename to examples/MPM/dataset_description.json 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 new file mode 100644 index 0000000..ad84b76 --- /dev/null +++ b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_MTsat.json @@ -0,0 +1,43 @@ +{"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/ds-04/sub-01/anat/sub-01_MTmap.nii.gz b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_MTsat.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_MTmap.nii.gz rename to examples/MPM/derivatives/hmri/sub-01/anat/sub-01_MTsat.nii.gz 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 new file mode 100644 index 0000000..ad84b76 --- /dev/null +++ b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_PDmap.json @@ -0,0 +1,43 @@ +{"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/ds-04/sub-01/anat/sub-01_PDmap.nii.gz b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_PDmap.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_PDmap.nii.gz rename to examples/MPM/derivatives/hmri/sub-01/anat/sub-01_PDmap.nii.gz 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 new file mode 100644 index 0000000..ad84b76 --- /dev/null +++ b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R1map.json @@ -0,0 +1,43 @@ +{"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/ds-04/sub-01/anat/sub-01_R1map.nii.gz b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R1map.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_R1map.nii.gz rename to examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R1map.nii.gz 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 new file mode 100644 index 0000000..ad84b76 --- /dev/null +++ b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R2starmap.json @@ -0,0 +1,43 @@ +{"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/ds-04/sub-01/anat/sub-01_R2starmap.nii.gz b/examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R2starmap.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_R2starmap.nii.gz rename to examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R2starmap.nii.gz diff --git a/examples/ds-04/sub-01/fmap/sub-01_B0map.json b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.json similarity index 82% rename from examples/ds-04/sub-01/fmap/sub-01_B0map.json rename to examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.json index ed26345..83aa41a 100644 --- a/examples/ds-04/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/ds-04/sub-01/anat/sub-01_echo-1_part-mag_MTw.nii.gz b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_echo-1_part-mag_MTw.nii.gz rename to examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B0map.nii.gz diff --git a/examples/ds-04/sub-01/fmap/sub-01_B1map.json b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.json similarity index 77% rename from examples/ds-04/sub-01/fmap/sub-01_B1map.json rename to examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.json index 34faae0..bd20163 100644 --- a/examples/ds-04/sub-01/fmap/sub-01_B1map.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/ds-04/sub-01/anat/sub-01_echo-1_part-mag_PDw.nii.gz b/examples/MPM/derivatives/hmri/sub-01/fmap/sub-01_B1plusmap.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_echo-1_part-mag_PDw.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_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..fa97178 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MToff_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0023, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", + "Modality": "MR", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma", + "InstitutionName": 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"%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", +} 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..da18d6b --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-MTon_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0023, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", + "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_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_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, + "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", +} 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..d895526 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-1_acq-T1w_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0023, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", + "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_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_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, + "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", +} diff --git a/examples/ds-04/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/ds-04/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/ds-04/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/ds-04/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/ds-04/sub-01/anat/sub-01_echo-2_part-mag_PDw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_echo-2_part-mag_PDw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-1_part-mag_acq-T1w_MPM.nii.gz 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 new file mode 100644 index 0000000..f374474 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MToff_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0046, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", + "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, + "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", +} 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 new file mode 100644 index 0000000..c3bf822 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-MTon_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0046, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", + "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_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_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, + "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", +} 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 new file mode 100644 index 0000000..3509c4d --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-2_acq-T1w_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0046, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", + "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_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_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, + "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", +} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-2_part-mag_T1w.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_echo-2_part-mag_T1w.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_acq-MToff_MPM.nii.gz diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-3_part-mag_MTw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_echo-3_part-mag_MTw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_acq-MTon_MPM.nii.gz diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-3_part-mag_PDw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_echo-3_part-mag_PDw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-2_part-mag_acq-T1w_MPM.nii.gz 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 new file mode 100644 index 0000000..00aca3b --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MToff_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0069, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", + "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, + "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", +} 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 new file mode 100644 index 0000000..cff35fa --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-MTon_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0069, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", + "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_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_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, + "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", +} 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 new file mode 100644 index 0000000..1da6a93 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-3_acq-T1w_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0069, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", + "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_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_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, + "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", +} diff --git a/examples/ds-04/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 examples/ds-04/sub-01/anat/sub-01_echo-3_part-mag_T1w.nii.gz.gz rename to examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-MToff_MPM.nii.gz diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-4_part-mag_MTw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_echo-4_part-mag_MTw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-MTon_MPM.nii.gz diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-4_part-mag_PDw.nii.gz b/examples/MPM/sub-01/anat/sub-01_echo-3_part-mag_acq-T1w_MPM.nii.gz similarity index 100% rename from examples/ds-04/sub-01/anat/sub-01_echo-4_part-mag_PDw.nii.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/anat/sub-01_echo-4_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json new file mode 100644 index 0000000..87f996e --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MToff_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0092, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", + "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, + "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", +} 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 new file mode 100644 index 0000000..443676b --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-MTon_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0092, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", + "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_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_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, + "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", +} 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 new file mode 100644 index 0000000..87c7583 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-4_acq-T1w_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0092, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", + "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_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_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, + "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", +} diff --git a/examples/ds-04/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/ds-04/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/ds-04/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/ds-04/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/ds-04/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/ds-04/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_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json new file mode 100644 index 0000000..caec479 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MToff_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", + "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, + "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", +} 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 new file mode 100644 index 0000000..e91e833 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-MTon_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", + "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_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_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, + "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", +} 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 new file mode 100644 index 0000000..3417069 --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-5_acq-T1w_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0115, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", + "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_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_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, + "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", +} diff --git a/examples/ds-04/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/ds-04/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/ds-04/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/ds-04/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/ds-04/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/ds-04/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_acq-MToff_MPM.json b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json new file mode 100644 index 0000000..4525e0c --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MToff_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0138, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", + "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, + "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", +} 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 new file mode 100644 index 0000000..7ce383c --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-MTon_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0138, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "On", + "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_MTw_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_MTw_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": 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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 new file mode 100644 index 0000000..3b1e03a --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-6_acq-T1w_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0138, + "RepetitionTime": 0.025, + "FlipAngle": 21, + "MTState" : "Off", + "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_T1w_GRAPPA4_PSN_488BW", + "ProtocolName": "mfc_3dflash_T1w_GRAPPA4_PSN_488BW", + "ScanningSequence": "RM", + "SequenceVariant": "SP", + "SequenceName": "fl3d_1i3d8", + "ImageType": 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b/examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_acq-MToff_MPM.nii.gz similarity index 100% rename from examples/ds-04/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/ds-04/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/ds-04/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/ds-04/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% rename from examples/ds-04/sub-01/anat/sub-01_echo-8_part-mag_PDw.nii.gz rename to examples/MPM/sub-01/anat/sub-01_echo-6_part-mag_acq-T1w_MPM.nii.gz diff --git a/examples/MPM/sub-01/anat/sub-01_echo-7_acq-MToff_MPM.json 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examples/ds-04/sub-01/fmap/sub-01_B1minusmap_MTw.gz rename to examples/MPM/sub-01/anat/sub-01_echo-7_part-mag_acq-MToff_MPM.nii.gz 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 new file mode 100644 index 0000000..f201e0e --- /dev/null +++ b/examples/MPM/sub-01/anat/sub-01_echo-8_acq-MToff_MPM.json @@ -0,0 +1,63 @@ +{ + "EchoTime": 0.0184, + "RepetitionTime": 0.025, + "FlipAngle": 6, + "MTState" : "Off", + "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": 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b/examples/MPM/sub-01/fmap/sub-01_echo-1_part-mag_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", 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"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/ds-04/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz b/examples/MPM/sub-01/fmap/sub-01_echo-2_B1plusmap.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_B1plusmap.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 new file mode 100644 index 0000000..d90e38c --- /dev/null +++ b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_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"] +} diff --git a/examples/MPM/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 new file mode 100644 index 0000000..4d66880 Binary files /dev/null and b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-mag_B0map.nii.gz differ 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 new file mode 100644 index 0000000..d90e38c --- /dev/null +++ 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"] +} diff --git a/examples/MPM/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 new file mode 100644 index 0000000..4d66880 Binary files /dev/null and b/examples/MPM/sub-01/fmap/sub-01_echo-2_part-phase_B0map.nii.gz differ diff --git a/examples/ds-01/sub-01/anat/sub-01_MEGRE.json b/examples/ds-01/sub-01/anat/sub-01_MEGRE.json deleted file mode 100644 index ba52a97..0000000 --- a/examples/ds-01/sub-01/anat/sub-01_MEGRE.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_QSM.json b/examples/ds-01/sub-01/anat/sub-01_QSM.json deleted file mode 100644 index bda495c..0000000 --- a/examples/ds-01/sub-01/anat/sub-01_QSM.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "BasedOn": [ - "anat/sub-01_echo-1_part-mag_FLASH.nii.gz", - "anat/sub-01_echo-1_part-phase_FLASH.nii.gz" - ], - "EstimationMethod": "Schaefer et al., 2011" -} diff --git a/examples/ds-01/sub-01/anat/sub-01_T2starmap.json b/examples/ds-01/sub-01/anat/sub-01_T2starmap.json deleted file mode 100644 index b159cd0..0000000 --- a/examples/ds-01/sub-01/anat/sub-01_T2starmap.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "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" - ], - "EstimationMethod": "Linear least-squares" -} diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-1_MEGRE.json b/examples/ds-01/sub-01/anat/sub-01_echo-1_MEGRE.json deleted file mode 100644 index 755f482..0000000 --- a/examples/ds-01/sub-01/anat/sub-01_echo-1_MEGRE.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.01 -} diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-2_MEGRE.json b/examples/ds-01/sub-01/anat/sub-01_echo-2_MEGRE.json deleted file mode 100644 index 3d2e5b4..0000000 --- a/examples/ds-01/sub-01/anat/sub-01_echo-2_MEGRE.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.02 -} diff --git a/examples/ds-01/sub-01/anat/sub-01_echo-3_MEGRE.json b/examples/ds-01/sub-01/anat/sub-01_echo-3_MEGRE.json deleted file mode 100644 index 6928485..0000000 --- a/examples/ds-01/sub-01/anat/sub-01_echo-3_MEGRE.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "EchoTime": 0.03 -} diff --git a/examples/ds-02/sub-01/anat/sub-01_MP2RAGE.json b/examples/ds-02/sub-01/anat/sub-01_MP2RAGE.json deleted file mode 100644 index 72f72f9..0000000 --- a/examples/ds-02/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/ds-02/sub-01/anat/sub-01_T1map.json b/examples/ds-02/sub-01/anat/sub-01_T1map.json deleted file mode 100644 index 2caede4..0000000 --- a/examples/ds-02/sub-01/anat/sub-01_T1map.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "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" -} diff --git a/examples/ds-02/sub-01/anat/sub-01_inv-1_MP2RAGE.json b/examples/ds-02/sub-01/anat/sub-01_inv-1_MP2RAGE.json deleted file mode 100644 index b1f0220..0000000 --- a/examples/ds-02/sub-01/anat/sub-01_inv-1_MP2RAGE.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "InversionTime": 0.8, - "FlipAngle": 5 -} diff --git a/examples/ds-02/sub-01/anat/sub-01_inv-2_MP2RAGE.json b/examples/ds-02/sub-01/anat/sub-01_inv-2_MP2RAGE.json deleted file mode 100644 index f6cb93d..0000000 --- a/examples/ds-02/sub-01/anat/sub-01_inv-2_MP2RAGE.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "InversionTime": 2.7, - "FlipAngle": 7 -} diff --git a/examples/ds-03/sub-01/anat/sub-01_MP2RAGE.json b/examples/ds-03/sub-01/anat/sub-01_MP2RAGE.json deleted file mode 100644 index 422d114..0000000 --- a/examples/ds-03/sub-01/anat/sub-01_MP2RAGE.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "NumberShots": 150, - "RepetitionTimeInversion": 6.723 -} diff --git a/examples/ds-03/sub-01/anat/sub-01_T1map.json b/examples/ds-03/sub-01/anat/sub-01_T1map.json deleted file mode 100644 index 54fceba..0000000 --- a/examples/ds-03/sub-01/anat/sub-01_T1map.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "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" -} diff --git a/examples/ds-03/sub-01/anat/sub-01_T2starmap.json b/examples/ds-03/sub-01/anat/sub-01_T2starmap.json deleted file mode 100644 index 3d0368d..0000000 --- a/examples/ds-03/sub-01/anat/sub-01_T2starmap.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "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" -} 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-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-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-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_inv-1_MP2RAGE.json b/examples/ds-03/sub-01/anat/sub-01_inv-1_MP2RAGE.json deleted file mode 100644 index 3b2187b..0000000 --- a/examples/ds-03/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/ds-03/sub-01/anat/sub-01_inv-2_MP2RAGE.json b/examples/ds-03/sub-01/anat/sub-01_inv-2_MP2RAGE.json deleted file mode 100644 index 18a74e4..0000000 --- a/examples/ds-03/sub-01/anat/sub-01_inv-2_MP2RAGE.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "InversionTime": 3.855, - "FlipAngle": 6, - "RepetitionTimeExcitation": 0.032 -} diff --git a/examples/ds-04/sub-01/anat/sub-01_MTmap.json b/examples/ds-04/sub-01/anat/sub-01_MTmap.json deleted file mode 100644 index 3529b6b..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_MTmap.json +++ /dev/null @@ -1,25 +0,0 @@ -{"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"} diff --git a/examples/ds-04/sub-01/anat/sub-01_MTw.json b/examples/ds-04/sub-01/anat/sub-01_MTw.json deleted file mode 100644 index e1fb09a..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_MTw.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/ds-04/sub-01/anat/sub-01_PDmap.json b/examples/ds-04/sub-01/anat/sub-01_PDmap.json deleted file mode 100644 index 7370b6c..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_PDmap.json +++ /dev/null @@ -1,26 +0,0 @@ -{"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"} diff --git a/examples/ds-04/sub-01/anat/sub-01_PDw.json b/examples/ds-04/sub-01/anat/sub-01_PDw.json deleted file mode 100644 index e1fb09a..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_PDw.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/ds-04/sub-01/anat/sub-01_R1map.json b/examples/ds-04/sub-01/anat/sub-01_R1map.json deleted file mode 100644 index 204d07c..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_R1map.json +++ /dev/null @@ -1,26 +0,0 @@ -{"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"} diff --git a/examples/ds-04/sub-01/anat/sub-01_R2starmap.json b/examples/ds-04/sub-01/anat/sub-01_R2starmap.json deleted file mode 100644 index 54013c8..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_R2starmap.json +++ /dev/null @@ -1,26 +0,0 @@ -{"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"} - diff --git a/examples/ds-04/sub-01/anat/sub-01_T1w.json b/examples/ds-04/sub-01/anat/sub-01_T1w.json deleted file mode 100644 index 7d4274d..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_T1w.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/ds-04/sub-01/anat/sub-01_echo-1_MTw.json b/examples/ds-04/sub-01/anat/sub-01_echo-1_MTw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-1_MTw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-1_PDw.json b/examples/ds-04/sub-01/anat/sub-01_echo-1_PDw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-1_PDw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-1_T1w.json b/examples/ds-04/sub-01/anat/sub-01_echo-1_T1w.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-1_T1w.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-2_MTw.json b/examples/ds-04/sub-01/anat/sub-01_echo-2_MTw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-2_MTw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-2_PDw.json b/examples/ds-04/sub-01/anat/sub-01_echo-2_PDw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-2_PDw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-2_T1w.json b/examples/ds-04/sub-01/anat/sub-01_echo-2_T1w.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-2_T1w.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-3_MTw.json b/examples/ds-04/sub-01/anat/sub-01_echo-3_MTw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-3_MTw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-3_PDw.json b/examples/ds-04/sub-01/anat/sub-01_echo-3_PDw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-3_PDw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-3_T1w.json b/examples/ds-04/sub-01/anat/sub-01_echo-3_T1w.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-3_T1w.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-4_MTw.json b/examples/ds-04/sub-01/anat/sub-01_echo-4_MTw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-4_MTw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-4_PDw.json b/examples/ds-04/sub-01/anat/sub-01_echo-4_PDw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-4_PDw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-4_T1w.json b/examples/ds-04/sub-01/anat/sub-01_echo-4_T1w.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-4_T1w.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-5_MTw.json b/examples/ds-04/sub-01/anat/sub-01_echo-5_MTw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-5_MTw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-5_PDw.json b/examples/ds-04/sub-01/anat/sub-01_echo-5_PDw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-5_PDw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-5_T1w.json b/examples/ds-04/sub-01/anat/sub-01_echo-5_T1w.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-5_T1w.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-6_MTw.json b/examples/ds-04/sub-01/anat/sub-01_echo-6_MTw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-6_MTw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-6_PDw.json b/examples/ds-04/sub-01/anat/sub-01_echo-6_PDw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-6_PDw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-6_T1w.json b/examples/ds-04/sub-01/anat/sub-01_echo-6_T1w.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-6_T1w.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-7_PDw.json b/examples/ds-04/sub-01/anat/sub-01_echo-7_PDw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-7_PDw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/anat/sub-01_echo-8_PDw.json b/examples/ds-04/sub-01/anat/sub-01_echo-8_PDw.json deleted file mode 100644 index 417be57..0000000 --- a/examples/ds-04/sub-01/anat/sub-01_echo-8_PDw.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.0147} diff --git a/examples/ds-04/sub-01/fmap/sub-01_B1minusmap_MTw.json b/examples/ds-04/sub-01/fmap/sub-01_B1minusmap_MTw.json deleted file mode 100644 index f89017c..0000000 --- a/examples/ds-04/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/ds-04/sub-01/fmap/sub-01_B1minusmap_PDw.json b/examples/ds-04/sub-01/fmap/sub-01_B1minusmap_PDw.json deleted file mode 100644 index bb8d9dc..0000000 --- a/examples/ds-04/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/ds-04/sub-01/fmap/sub-01_B1minusmap_T1w.json b/examples/ds-04/sub-01/fmap/sub-01_B1minusmap_T1w.json deleted file mode 100644 index 9542f67..0000000 --- a/examples/ds-04/sub-01/fmap/sub-01_B1minusmap_T1w.json +++ /dev/null @@ -1,7 +0,0 @@ -{"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"] -} diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-1_B1map.json b/examples/ds-04/sub-01/fmap/sub-01_echo-1_B1map.json deleted file mode 100644 index 1b3b43c..0000000 --- a/examples/ds-04/sub-01/fmap/sub-01_echo-1_B1map.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime”: 0.03706} diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-1_part-mag_B0map.json b/examples/ds-04/sub-01/fmap/sub-01_echo-1_part-mag_B0map.json deleted file mode 100644 index 9561d0b..0000000 --- a/examples/ds-04/sub-01/fmap/sub-01_echo-1_part-mag_B0map.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.01} diff --git a/examples/ds-04/sub-01/fmap/sub-01_echo-2_B1map.json b/examples/ds-04/sub-01/fmap/sub-01_echo-2_B1map.json deleted file mode 100644 index b7d1e8d..0000000 --- a/examples/ds-04/sub-01/fmap/sub-01_echo-2_B1map.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime”: 0.01853} diff --git a/examples/ds-04/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 deleted file mode 100644 index 6546cbd..0000000 --- a/examples/ds-04/sub-01/fmap/sub-01_echo-2_part-mag_B0map.json +++ /dev/null @@ -1 +0,0 @@ -{"EchoTime": 0.01246} diff --git a/examples/ds-04/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 deleted file mode 100644 index e69de29..0000000