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Add curation script for INSPIRED dataset BIDSification #185

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08786fe
Add python script for conversion of INSPIRED dataset to BIDS complian…
valosekj Nov 29, 2022
37038dc
Implement MPM image BIDSification
valosekj Nov 29, 2022
336ad10
Make sure that input args have abs path
valosekj Nov 29, 2022
3e231d3
Match also upper case in MPM json sidecars
valosekj Nov 29, 2022
0df6da5
Fix condition when there are no json sidecars for MPM images
valosekj Nov 29, 2022
0c17d8c
Save conversion progress to log
valosekj Nov 30, 2022
1814879
Write participants.tsv file
valosekj Nov 30, 2022
36a5b89
Comments clarification
valosekj Nov 30, 2022
6a07373
Create participants.json, dataset_description.json, and README files.…
valosekj Dec 2, 2022
1c2d836
Use ISO-8859-1 encoding to open json files
valosekj Dec 4, 2022
71c6eb0
Sort subjects in participants.tsv; fix typo in participants.json
valosekj Dec 4, 2022
13ecab1
Keep only .tar.gz subjects in the input dataset
valosekj Dec 4, 2022
ad2e658
Remove solved TODO
valosekj Dec 5, 2022
31df28e
Add usage example
valosekj Dec 5, 2022
581edc0
Remove function for automatic README creation.
valosekj Dec 12, 2022
09e12ed
Keep the original subjectID
valosekj Dec 12, 2022
2ce0afd
Create .bidsignore to exclude `bp-cspine` tag from bids-validator
valosekj Dec 12, 2022
a2c5bba
Fix bug in subject_id variable construction
valosekj Dec 12, 2022
8556af9
Add README for inspired dataset
valosekj Dec 12, 2022
30ae997
Switch from `bp-cspine` to `acq-cspine`
valosekj Dec 21, 2022
b364bf5
Deal with SC derivatives
valosekj Dec 21, 2022
cf60790
Use label-SC_mask, label-WM_mask, and label-GM_mask
valosekj Jan 4, 2023
0d135cc
Include DatasetType (raw or derivative) to dataset_description.json.
valosekj Jan 4, 2023
1b52867
Update participants.tsv and participants.json
valosekj Jan 4, 2023
65e56e1
Add script for merge of participants.tsv and table with clinical DCM …
valosekj Jan 4, 2023
5a39c77
Rename data_id to source_id to be compatible with participants.tsv
valosekj Jan 4, 2023
1151061
Use n/a for empty cells
valosekj Jan 4, 2023
374876a
Add leading zeros to source_id and institution_id (to match with the …
valosekj Jan 4, 2023
8959d2c
Clarify script description
valosekj Jan 4, 2023
6d3a956
Rename derivatives/labels to derivatives/manual_labels
valosekj Jan 6, 2023
a81a8ef
Copy qform to sform
valosekj Jan 20, 2023
4fbc4bf
Swap 'dir-AP_acq-cspine' to 'acq-cspine_dir-AP' to pass bids-validator
valosekj Jan 21, 2023
f529249
Change '_mask' to '_seg'
valosekj Jan 21, 2023
b5a7b5f
Rename README to README.md and update it.
valosekj Jan 21, 2023
33f440a
Update 'participants.json' according to https://intranet.neuro.polymt…
valosekj Jan 21, 2023
e17ed2c
README.md update
valosekj Jan 21, 2023
9941af1
Move infolink
valosekj Jan 24, 2023
7d97836
Add Contact Person section
valosekj Jan 24, 2023
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35 changes: 35 additions & 0 deletions scripts/README.md
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# INSPIRED

This is an MRI dataset acquired in the context of the INSPIRED project (https://www.spinalsurgerynews.com/2016/10/inspired-spinal-cord-neuro-imaging-project/14594).

It contains brain and spinal cord data acquired at two sites centers (Toronto, Zurich) from healthy controls (HC) and two pathologies:
- degenerative cervical myelopathy (DCM)
- spinal cord injury (SCI)

It also contains spinal cord segmentation for T2w axial images and gray matter and white matter segmentations for T2star images.

## Dataset structure

Spinal cord MRI data:
- T1w
- T2w axial
- T2w sagittal
- T2star
- DWI (A-P and P-A phase encoding)

Brain MRI data:
- MPM (multi-parameter mapping)
- DWI (A-P and P-A phase encoding)

## Naming convention

sub-<site><pathology>XXX

Note: BIDS label `acq-cspine` is used to differentiate spine images from brain. For details, see https://github.com/neuropoly/data-management/pull/185#issuecomment-1362069079.

Note: 01 corresponds to Toronto site, 02 to Zurich site. For details, see https://github.com/neuropoly/data-management/issues/184#issuecomment-1329250514.

## Contact Person

Main PI of the project: Claudia Wheeler Kingshott
Contact person: Julien Cohen-Adad
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