Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[FIX] use bids uri for qmri derivatives #339

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

[FIX] use bids uri for qmri derivatives #339

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion qmri_mpm/derivatives/hmri/dataset_description.json
View file
Open in desktop
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": "../../"
Remi-Gau marked this conversation as resolved.
Show resolved Hide resolved
}
}

12 changes: 6 additions & 6 deletions qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-MTw_RB1map.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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",
Expand Down
16 changes: 8 additions & 8 deletions qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-PDw_RB1map.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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",
Expand Down
16 changes: 8 additions & 8 deletions qmri_mpm/derivatives/hmri/sub-01/fmap/sub-01_acq-T1w_RB1map.json
View file
Open in desktop
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",
Expand Down
5 changes: 4 additions & 1 deletion qmri_mtsat/derivatives/qMRLab/dataset_description.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,5 +9,8 @@
"Name": "Manual",
"Description": "Adapted from existing example, adjusted to conform to BIDS Derivatives"
}
]
],
"DatasetLinks": {
"source": "../../"
Remi-Gau marked this conversation as resolved.
Show resolved Hide resolved
}
}
4 changes: 2 additions & 2 deletions qmri_mtsat/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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"
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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"
Expand Down
5 changes: 4 additions & 1 deletion qmri_vfa/derivatives/qMRLab/dataset_description.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,5 +14,8 @@
"Name": "Manual",
"Description": "Adjusted to conform to BIDS Derivatives"
}
]
],
"DatasetLinks": {
"source": "../../"
Remi-Gau marked this conversation as resolved.
Show resolved Hide resolved
}
}
2 changes: 1 addition & 1 deletion qmri_vfa/derivatives/qMRLab/sub-01/fmap/sub-01_TB1map.json
View file
Open in desktop
Original file line number Diff line number Diff line change
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",
Expand Down