I am using the open dataset called OASIS-3. I would like to process it using fMRIPrep toolbox, but it works only with BIDS validated dataset. The data for one patient in OASIS dataset is organized like this:
+---anat2 | +---BIDS | | sub-OAS30457_ses-d0102_run-01_T1w.json | | | \---NIFTI | sub-OAS30457_ses-d0102_run-01_T1w.nii.gz | +---anat3 | +---BIDS | | sub-OAS30457_ses-d0102_run-02_T1w.json | | | \---NIFTI | sub-OAS30457_ses-d0102_run-02_T1w.nii.gz | +---BIDS | dataset_description.json | +---dwi1 | +---BIDS | | sub-OAS30457_ses-d0102_dwi.bval | | sub-OAS30457_ses-d0102_dwi.bvec | | sub-OAS30457_ses-d0102_dwi.json | | | \---NIFTI | sub-OAS30457_ses-d0102_dwi.nii.gz | +---func1 | +---BIDS | | sub-OAS30457_ses-d0102_task-rest_run-01_bold.json | | | \---NIFTI | sub-OAS30457_ses-d0102_task-rest_run-01_bold.nii.gz | +---func2 | +---BIDS | | sub-OAS30457_ses-d0102_task-rest_run-02_bold.json | | | \---NIFTI | sub-OAS30457_ses-d0102_task-rest_run-02_bold.nii.gz |
In terms of BIDS specification the filenames are fine, I think. However, the general structure of folders and sub-folders are not really in BIDS format. I have checked the dataset_description.json file and it says (more details are provided in pdf file here):
“HowToAcknowledge”: “Refer to documentation at www.oasis-brains.org”,
“License”: “Refer to Data Use Agreement at www.oasis-brains.org”,
I am a little bit confused here, but I think that the dataset probably in the older version of BIDS which is really different from the latest one. That is why it looks like the BIDS dataset, but not exactly - because of the version differences.
Since I am not so experienced user of BIDS, I see two options (1) write a script which can re-organize the folders structure to make it validated for BIDS, but it is can be very time consuming; (2) “upgrade” the dataset to newer BIDS version using ready solutions, but I am not sure that such things exist.
Do you have any ideas?
Any information and comments are useful