A colleague will be sending me a series of nifti files converted with dcm2niix, along with their .json side-cars. These would be single participant, single session. Does there exist a tool that organizes nifti+json pairs into a bids structure, or would this be something I simply need to do manually? …

[image] Reorganizing NifTI to BIDS Hi everyone. I have a set of DCM files that have already been converted with dcm2nii. Is there a standardized script available that then reorganizes those into a BIDS format? Thanks.

From a colleague in Paris: [image] GitHub - benoitberanger/niix2bids: Automatic BIDS architecture Automatic BIDS architecture. Contribute to benoitberanger/niix2bids development by creating an account on GitHub.

Here is a list of software available for BIDS conversion : https://bids.neuroimaging.io/benefits#mri-and-pet-converters https://github.com/benoitberanger/niix2bids has different objective : it is made for fast BIDS conversion but has to cut some corners. And It only works for Siemens magnets for no…

For one-offs or small datasets I usually do the conversion semi-manually, with an R script like below. Part of why I prefer this manual style is to be able to double-check the conversion (having an explicit record of which scans were assigned which names can be invaluable). Some programs create reco…

@benoitberanger the dcm2niix source code contains some hints on deriving modality from a Siemens MRI using the DICOM sequence name (0018,0024) which is stored as SequenceName in the BIDS JSON: ep_b: dwi epfid2d: perf epfid2d: bold epfid3d1_15: swi epse2d: dwi (when b-vals specified) epse2d: fmap (…

@neurolabusc thanks, this list will be useful for the decision tree niix2bids/config_file/siemens.py

@benoitberanger I will add your repo to the list of “converters” on the BIDS website.

@Remi-Gau The converter is not tested intensively. Is it ok to wait before adding it on the website ? In the next weeks/months I should have access to some large datasets from other MRI labs. This will help me check the robustness of the code.

@benoitberanger I have archived Siemens data that you might find useful. Most of my archives are designed to examine specific issues rather than typical datasets. However, you may find them useful. You can look at my OSF datasets , archival data , and many of my dcm_qa validation datasets e.g. dcm_qa_…

oh yeah of course. just ping me when you feel OK having it listed there.

Niifti conversion to BIDS?

JohnAtl June 23, 2022, 9:00pm 2

BIDS from DICOMS with automatic config file