Does fmriprep output/save the transformation matrices during the call to mcflirt?

Answer from Oscar Esteban:

Yes, fMRIPrep writes a text file containing all realignment matrices in ITK format.

Thanks for posting this here.

I’ve been double checking the correctness of my response and it seems that is not true. We definitely generate such text file with the list of realignment matrices in ITK format as an intermediate result, but we don’t seem to write it out anywhere.

Could you open a request in our repository?