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?



Hey @MunamWasi,

heudiconv and BidsConverter should be very helpful!

HTH, best, Peer


If you still have access to DICOMs I would recommend converting them again using one of the solutions listed here: Convert data to BIDS format This will allow you to automatically extract much more metadata than is present in your NIfTIs.

Otherwise I don’t know of an existing script to do that for any arbitrary input organization of NIfTIs, but writing such script tailored to your input organization should be straightforward.


Hi @PeerHerholz,

Thanks for the suggestions. I’m looking through how those works, but, my problem is that I no longer have the DICOM files available. Is there a workaround step that I should be looking at?



Hi @ChrisGorgolewski,

I appreciate your help here.

I do not have the original DICOMs anymore. Is there anything that I should look out for considering that I will be missing a lot of metadata?



Just try to dig up the scanning protocols to confirm that the RepetitionTime is correct (this one is stored in the nifti headers, but some old converters did not save it correctly) and optionally try to figure out what is the SliceTiming. Good luck!


Hey @MunamWasi,

sorry for the late reply. I can’t think of any predefined workaround step right now.
But, this is what @ChrisGorgolewski mentioned: a small script that reorganizes your data
tailored to your structure should be straightforward and done quickly.

Best, Peer


Hi @MunamWasi,
Was reorganizing NII to BIDS successful? if yes, could you please share your experience?


Hello @Relyativist. I ended up using a tool called MRIcroGL. I was able to do both my pre-processing and was able to do the BIDS conversion successfully through that.


@MunamWasi thank for your reply. But, i there is no such option in MRIcroGL as convert to BIDS, it only supports dcm2niix as i remember.