Convert data to BIDS format

[rmaatoug]

Hi guys,

I would like to know if someone has a very generic script I could use to convert my data to BIDS format.
My script is not the most efficient and every time I use an other data structure, I have to re-do some modification on the script.
It is very time consuming and not very efficient.

I would really appreciate,
Thanks,

[ChrisGorgolewski]

Solutions I know of:

Going from DICOMS to BIDS datasets (with folder structure):

• https://github.com/nipy/heudiconv
• https://github.com/cbedetti/Dcm2Bids
• https://github.com/jmtyszka/bidskit
• https://github.com/dangom/dac2bids

Going from DICOMS to NIFTI + BIDS JSON sidecar:

• https://github.com/rordenlab/dcm2niix
• https://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter--nifti-tool-and-viewer

Going from old OpenfMRI format to BIDS:

• https://github.com/INCF/openfmri2bids

Going from HCP to BIDS:

• https://github.com/suyashdb/hcp2bids

[rmaatoug]

Thank you very much,
Will be very helpful !

[Johan]

My fork of dcm2bids is feature complete for fMRI - given the right inputs you can generate a bids dataset that passes the validator with one call.

://github.com/jooh/Dcm2Bids

[ChrisGorgolewski]

You should also check out this series of tutorials: http://reproducibility.stanford.edu/bids-tutorial-series-part-1a/

[mobilette]

I guess you could also use BIDS'em ALL if you want a simple multiplatform dicom to BIDS converter.

It is not as “configurable” compared to the other but do the job.