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[FIX] use bids uri for qmri derivatives #339

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[FIX] use bids uri for qmri derivatives #339

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529fac8
use bids uri for mpm derivatives
Remi-Gau Oct 29, 2022
ccebff4
apply URI for other qmri datasets
Remi-Gau Oct 29, 2022
28231df
Apply suggestions from code review
Remi-Gau Nov 8, 2022
6494495
Apply suggestions from code review
Remi-Gau Jan 2, 2023
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5 changes: 4 additions & 1 deletion qmri_mpm/derivatives/hmri/dataset_description.json
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,9 @@
"https://doi.org/10.1016/j.dib.2019.104132",
"https://doi.org/10.1016/j.neuroimage.2019.01.029",
"https://doi.org/10.1016/j.dib.2019.104132"
]
],
"DatasetLinks": {
"source": "../../"
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}
}

12 changes: 6 additions & 6 deletions qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-MTw_RB1map.json
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@@ -1,11 +1,11 @@
{
"IntendedFor": [
"anat/sub-01_acq-MTw_echo-1_flip-1_mt-on_MPM.nii",
"anat/sub-01_acq-MTw_echo-2_flip-1_mt-on_MPM.nii",
"anat/sub-01_acq-MTw_echo-3_flip-1_mt-on_MPM.nii",
"anat/sub-01_acq-MTw_echo-4_flip-1_mt-on_MPM.nii",
"anat/sub-01_acq-MTw_echo-5_flip-1_mt-on_MPM.nii",
"anat/sub-01_acq-MTw_echo-6_flip-1_mt-on_MPM.nii"
"bids:source:sub-01/anat/sub-01_acq-MTw_echo-1_flip-1_mt-on_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-MTw_echo-2_flip-1_mt-on_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-MTw_echo-3_flip-1_mt-on_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-MTw_echo-4_flip-1_mt-on_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-MTw_echo-5_flip-1_mt-on_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-MTw_echo-6_flip-1_mt-on_MPM.nii"
],
"RawSources": [
"sub-01/fmap/sub-01_acq-bodyMTw_RB1COR.nii",
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16 changes: 8 additions & 8 deletions qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-PDw_RB1map.json
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@@ -1,13 +1,13 @@
{
"IntendedFor": [
"anat/sub-01_acq-PDw_echo-1_flip-1_mt-off_MPM.nii",
"anat/sub-01_acq-PDw_echo-2_flip-1_mt-off_MPM.nii",
"anat/sub-01_acq-PDw_echo-3_flip-1_mt-off_MPM.nii",
"anat/sub-01_acq-PDw_echo-4_flip-1_mt-off_MPM.nii",
"anat/sub-01_acq-PDw_echo-5_flip-1_mt-off_MPM.nii",
"anat/sub-01_acq-PDw_echo-6_flip-1_mt-off_MPM.nii",
"anat/sub-01_acq-PDw_echo-7_flip-1_mt-off_MPM.nii",
"anat/sub-01_acq-PDw_echo-8_flip-1_mt-off_MPM.nii"
"bids:source:sub-01/anat/sub-01_acq-PDw_echo-1_flip-1_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-PDw_echo-2_flip-1_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-PDw_echo-3_flip-1_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-PDw_echo-4_flip-1_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-PDw_echo-5_flip-1_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-PDw_echo-6_flip-1_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-PDw_echo-7_flip-1_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-PDw_echo-8_flip-1_mt-off_MPM.nii"
],
"RawSources": [
"sub-01/fmap/sub-01_acq-bodyPDw_RB1COR.nii",
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16 changes: 8 additions & 8 deletions qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-T1w_RB1map.json
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
{
"IntendedFor": [
"anat/sub-01_acq-T1w_echo-1_flip-2_mt-off_MPM.nii",
"anat/sub-01_acq-T1w_echo-2_flip-2_mt-off_MPM.nii",
"anat/sub-01_acq-T1w_echo-3_flip-2_mt-off_MPM.nii",
"anat/sub-01_acq-T1w_echo-4_flip-2_mt-off_MPM.nii",
"anat/sub-01_acq-T1w_echo-5_flip-2_mt-off_MPM.nii",
"anat/sub-01_acq-T1w_echo-6_flip-2_mt-off_MPM.nii",
"anat/sub-01_acq-T1w_echo-7_flip-2_mt-off_MPM.nii",
"anat/sub-01_acq-T1w_echo-8_flip-2_mt-off_MPM.nii"
"bids:source:sub-01/anat/sub-01_acq-T1w_echo-1_flip-2_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-T1w_echo-2_flip-2_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-T1w_echo-3_flip-2_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-T1w_echo-4_flip-2_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-T1w_echo-5_flip-2_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-T1w_echo-6_flip-2_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-T1w_echo-7_flip-2_mt-off_MPM.nii",
"bids:source:sub-01/anat/sub-01_acq-T1w_echo-8_flip-2_mt-off_MPM.nii"
],
"RawSources": [
"sub-01/fmap/sub-01_acq-bodyT1w_RB1COR.nii",
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5 changes: 4 additions & 1 deletion qmri_mtsat/derivatives/qMRLab/dataset_description.json
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Expand Up @@ -9,5 +9,8 @@
"Name": "Manual",
"Description": "Adapted from existing example, adjusted to conform to BIDS Derivatives"
}
]
],
"DatasetLinks": {
"source": "../../"
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}
}
4 changes: 2 additions & 2 deletions qmri_mtsat/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json
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@@ -1,7 +1,7 @@
{
"RawSources": [
"sub-01/fmap/sub-01_flip-01_TB1DAM.nii.gz",
"sub-01/fmap/sub-01_flip-02_TB1DAM.nii.gz"
"bids:source:sub-01/sub-01/fmap/sub-01_flip-01_TB1DAM.nii.gz",
"bids:source:sub-01/sub-01/fmap/sub-01_flip-02_TB1DAM.nii.gz"
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I think RawSources does not permit BIDS URIs, only dataset relative links. Also, that field is deprecated in favor of Sources (which does permit BIDS URIs)

https://bids-specification.readthedocs.io/en/latest/glossary.html#rawsources-metadata

I think we should either just use relative links here, OR turn the RawSources here into Sources

],
"IntendedFor": [
"anat/sub-01_T1map.nii.gz"
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5 changes: 4 additions & 1 deletion qmri_vfa/derivatives/qMRLab/dataset_description.json
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Expand Up @@ -14,5 +14,8 @@
"Name": "Manual",
"Description": "Adjusted to conform to BIDS Derivatives"
}
]
],
"DatasetLinks": {
"source": "../../"
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}
}
2 changes: 1 addition & 1 deletion qmri_vfa/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json
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Expand Up @@ -3,7 +3,7 @@
"sub-01/fmap/sub-01_acq-tr2_TB1AFI.nii.gz"
],
"IntendedFor": [
"anat/sub-01_T1map.nii.gz"
"bids:source:sub-01/anat/sub-01_T1map.nii.gz"
],
"MagneticFieldStrength": "3",
"Manufacturer": "Siemens",
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