I have used fMRIprep for preprocessing of rsfMRI data. My input data to fMRIprep for preprocessing includes whole brain EPI and subject’s T1. And now I want to register fMRIprep output BOLD which has been registered to T1, to subject’s T2 image. Subject’s T2 image is not whole brain and I have segmentations in T2 space that I would like to use. I am trying to combine transformation that fMRIprep outputs, sub-participant _ses-02_task-rest_from-scanner_to-T1w_mode-image_xfm.txt, with a transformation that I have computed using fsl flirt for taking T1 to T2 space, to create a transformation that takes rsfMRI to T2 space. However, the fMRIprep xfm.txt format looks different and convert_xfm gives me an error when I feed these 2 transformations to it. Is there any command or method in fMRIprep that I could use to convert fmri prep transformations to fsl transformation conventions?
Dear Joerg,
Thanks for answering my question. I really appreciate it.
I tried converting the sub-participant _ses-02_task-rest_from-scanner_to-T1w_mode-image_xfm.txt with niworkflows.interfaces.nitransforms.concatenate_xfms in python.
But I was really confused how to use it. I was wondering if you have any examples of commands that you used before. Again many thanks.