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Created 'derivatives' folder with processed MPM output #38

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Created 'derivatives' folder with processed MPM output #38

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05224b4
Created 'derivatives' folder with processed MPM output
Apr 11, 2019
c0fe1ed
Restructured all 4 examples to have 'derivatives' and 'sourcedata' ma…
Apr 11, 2019
6b7d1c8
Move example RAW data from SOURCE data
KirstieJane Apr 15, 2019
b140377
Move derivatives files in ds-4 to an hmri pipeline folder
KirstieJane Apr 15, 2019
6fb08a2
Merge pull request #1 from KirstieJane/lazaral-master
Apr 19, 2019
2cc6d07
Made clearer names for "ds-01/2/3/4" folders; pipeline names in deriv…
Apr 19, 2019
2c716cd
Integrated suggested explanation for avoiding FLASH/MEGRE suffix in t…
Apr 22, 2019
56d6370
Merge pull request #2 from bids-standard/master
May 27, 2019
33f69cb
Fixed MPM and MEGRE examples, added sequence suffix to raw data
May 28, 2019
6b36153
Merge branch 'master' of https://github.com/bids-standard/bep001 into…
KirstieJane Jul 25, 2019
2ce5fb6
Merge branch 'lazaral-master'
KirstieJane Jul 25, 2019
1ecae5d
Removed extra json files to be compliant with the inheritance princip…
Sep 15, 2019
b013898
added details to MPM scan jsons
Sep 16, 2019
0201643
updated json files for MP2RAGE_singleecho
Sep 27, 2019
ce73f3e
updated json files for MP2RAGE_multiecho
Sep 27, 2019
c4d09cf
updated jsons for MPM fieldmaps
Sep 27, 2019
9183c89
created realistic json for MPM echoes
Sep 27, 2019
9f83abd
MEGRE json expansion
Sep 27, 2019
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22 changes: 22 additions & 0 deletions examples/BEP001_examples.md
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# 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.*
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Awesome!



## 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.
2 changes: 1 addition & 1 deletion examples/ds-01/dataset_description.json → .../MEGRE_multiecho/dataset_description.json
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"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."
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This is a great change ✅

This is what I was thinking of when I said add the information to the dataset_description.json file - adding the text you have describing the dataset in the BEP001_examples.md file to the json itself 😄

}
7 changes: 7 additions & 0 deletions examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_QSM.json
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{
"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"
}
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8 changes: 8 additions & 0 deletions examples/MEGRE_multiecho/derivatives/qsm_pipeline/sub-01/anat/sub-01_T2starmap.json
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{
"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"
}
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9 changes: 9 additions & 0 deletions examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-1_MEGRE.json
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{
"IntendedFor": ["anat/sub-01_T2starmap.nii.gz",
"anat/sub-01_QSM.nii.gz"],
"MagneticFieldStrength": "3",
"Manufacturer": "GE",
"PulseSequenceType": "SPGR",
"RepetitionTime": "0.0150",
"FlipAngle": "3"
}
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9 changes: 9 additions & 0 deletions examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-2_MEGRE.json
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{
"IntendedFor": ["anat/sub-01_T2starmap.nii.gz",
"anat/sub-01_QSM.nii.gz"],
"MagneticFieldStrength": "3",
"Manufacturer": "GE",
"PulseSequenceType": "SPGR",
"RepetitionTime": "0.0150",
"FlipAngle": "3"
}
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9 changes: 9 additions & 0 deletions examples/MEGRE_multiecho/sub-01/anat/sub-01_echo-3_MEGRE.json
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{
"IntendedFor": ["anat/sub-01_T2starmap.nii.gz",
"anat/sub-01_QSM.nii.gz"],
"MagneticFieldStrength": "3",
"Manufacturer": "GE",
"PulseSequenceType": "SPGR",
"RepetitionTime": "0.0150",
"FlipAngle": "3"
}
0 .../anat/sub-01_echo-3_part-mag_MEGRE.nii.gz → .../anat/sub-01_echo-3_part-mag_MEGRE.nii.gz
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0 examples/ds-03/dataset_description.json → ...P2RAGE_multiecho/dataset_description.json
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16 changes: 16 additions & 0 deletions examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json
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{
"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"
}
0 ...les/ds-02/sub-01/anat/sub-01_T1map.nii.gz → ...s/mp2rage/sub-01/anat/sub-01_T1map.nii.gz
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12 changes: 12 additions & 0 deletions examples/MP2RAGE_multiecho/derivatives/mp2rage/sub-01/anat/sub-01_T2starmap.json
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{
"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"
}
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7 changes: 7 additions & 0 deletions examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json
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{
"InversionTime": 0.67,
"FlipAngle": 7,
"ExcitationRepetitionTime": 0.0062,
"InversionRepetitionTime": 6.723,
"NumberShots": 150
}
8 changes: 8 additions & 0 deletions examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-1_MP2RAGE.json
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{
"InversionTime": 3.855,
"FlipAngle": 6,
"ExcitationRepetitionTime": 0.032,
"InversionRepetitionTime": 6.723,
"NumberShots": 150,
"EchoTime": 0.006
}
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8 changes: 8 additions & 0 deletions examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-2_MP2RAGE.json
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{
"InversionTime": 3.855,
"FlipAngle": 6,
"ExcitationRepetitionTime": 0.032,
"InversionRepetitionTime": 6.723,
"NumberShots": 150,
"EchoTime": 0.0145
}
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8 changes: 8 additions & 0 deletions examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-3_MP2RAGE.json
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{
"InversionTime": 3.855,
"FlipAngle": 6,
"ExcitationRepetitionTime": 0.032,
"InversionRepetitionTime": 6.723,
"NumberShots": 150,
"EchoTime": 0.0230
}
0 ...b-01_echo-1_inv-2_part-mag_MP2RAGE.nii.gz → ...b-01_inv-2_echo-3_part-mag_MP2RAGE.nii.gz
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8 changes: 8 additions & 0 deletions examples/MP2RAGE_multiecho/sub-01/anat/sub-01_inv-2_echo-4_MP2RAGE.json
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{
"InversionTime": 3.855,
"FlipAngle": 6,
"ExcitationRepetitionTime": 0.032,
"InversionRepetitionTime": 6.723,
"NumberShots": 150,
"EchoTime": 0.0315
}
0 ...b-01_echo-2_inv-2_part-mag_MP2RAGE.nii.gz → ...b-01_inv-2_echo-4_part-mag_MP2RAGE.nii.gz
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0 ...01_echo-2_inv-2_part-phase_MP2RAGE.nii.gz → ...01_inv-2_echo-4_part-phase_MP2RAGE.nii.gz
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0 examples/ds-03/sub-01/fmap/sub-01_B1map.json → ...E_multiecho/sub-01/fmap/sub-01_B1map.json
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0 ...les/ds-03/sub-01/fmap/sub-01_B1map.nii.gz → ...multiecho/sub-01/fmap/sub-01_B1map.nii.gz
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0 examples/ds-02/dataset_description.json → ...2RAGE_singleecho/dataset_description.json
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14 changes: 14 additions & 0 deletions examples/MP2RAGE_singleecho/derivatives/mp2rage/sub-01/anat/sub-01_T1map.json
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{
"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"
}
0 ...b-01_echo-3_inv-2_part-mag_MP2RAGE.nii.gz → ...s/mp2rage/sub-01/anat/sub-01_T1map.nii.gz
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0 examples/ds-02/sub-01/anat/sub-01_T1w.json → ...GE_singleecho/sub-01/anat/sub-01_T1w.json
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7 changes: 7 additions & 0 deletions examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-1_MP2RAGE.json
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{
"InversionTime": 0.8,
"FlipAngle": 5,
"ExcitationRepetitionTime": 0.0062,
"InversionRepetitionTime": 5.5,
"NumberShots": 159
}
0 ...anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz → ...anat/sub-01_inv-1_part-mag_MP2RAGE.nii.gz
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7 changes: 7 additions & 0 deletions examples/MP2RAGE_singleecho/sub-01/anat/sub-01_inv-2_MP2RAGE.json
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{
"InversionTime": 2.7,
"FlipAngle": 7,
"ExcitationRepetitionTime": 0.0062,
"InversionRepetitionTime": 5.5,
"NumberShots": 159
}
0 ...b-01_echo-4_inv-2_part-mag_MP2RAGE.nii.gz → ...anat/sub-01_inv-2_part-mag_MP2RAGE.nii.gz
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0 examples/ds-04/dataset_description.json → examples/MPM/dataset_description.json
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43 changes: 43 additions & 0 deletions examples/MPM/derivatives/hmri/sub-01/anat/sub-01_MTsat.json
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{"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"
}
0 ...les/ds-04/sub-01/anat/sub-01_MTmap.nii.gz → ...ives/hmri/sub-01/anat/sub-01_MTsat.nii.gz
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43 changes: 43 additions & 0 deletions examples/MPM/derivatives/hmri/sub-01/anat/sub-01_PDmap.json
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{"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"
}
0 ...les/ds-04/sub-01/anat/sub-01_PDmap.nii.gz → ...ives/hmri/sub-01/anat/sub-01_PDmap.nii.gz
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43 changes: 43 additions & 0 deletions examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R1map.json
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{"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"
}
0 ...les/ds-04/sub-01/anat/sub-01_R1map.nii.gz → ...ives/hmri/sub-01/anat/sub-01_R1map.nii.gz
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43 changes: 43 additions & 0 deletions examples/MPM/derivatives/hmri/sub-01/anat/sub-01_R2starmap.json
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{"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"
}
0 ...ds-04/sub-01/anat/sub-01_R2starmap.nii.gz → .../hmri/sub-01/anat/sub-01_R2starmap.nii.gz
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2 changes: 1 addition & 1 deletion examples/ds-04/sub-01/fmap/sub-01_B0map.json → ...atives/hmri/sub-01/fmap/sub-01_B0map.json
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{"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,
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0 ...01/anat/sub-01_echo-1_part-mag_MTw.nii.gz → ...ives/hmri/sub-01/fmap/sub-01_B0map.nii.gz
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2 changes: 1 addition & 1 deletion examples/ds-04/sub-01/fmap/sub-01_B1map.json → ...es/hmri/sub-01/fmap/sub-01_B1plusmap.json
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@@ -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"]}
0 ...01/anat/sub-01_echo-1_part-mag_PDw.nii.gz → .../hmri/sub-01/fmap/sub-01_B1plusmap.nii.gz
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