Volume to surface transform with fMRIPrep outputs


I am trying to use fMRIPrep outputs in volume space (_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz) and transform this to freesurfer (fsaverage) surface space.

I have found other threads regarding this (here), however my understanding is that mri_vol2surf resamples the data and we do not want resampling. So I am looking to only coregister the data.

Looking at another thread, it looks like I can use the *T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5 transform the image from MNI to subject space using antsApplyTransforms.

However, I haven’t had any luck finding a way to go from subject space to fsaverage surface space without resampling.

Any suggestions for the best way to perform this transform would be greatly appreciated.


Hi all,

Following up on this question. I am able to use antsApplyTransforms to transform the fMRIprep preprocessed T1w image from MNI space to subject space with the following command:

antsApplyTransforms -d 3 --verbose 1 \
--i /Users/hannah/Desktop/study/derivatives/fmriprep/sub-XXXX/ses-01/anat/sub-XXXX_ses-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz \
-o /Users/hannah/Desktop/study/derivatives/fmriprep/sub-XXXX/ses-01/anat/sub-XXXX_T1w_preproc_subject.nii.gz \
-r /Uses/hannah/Desktop/study/rawdata/sub-XXXX/ses-01/anat/sub-7092_ses-01_T1w.nii.gz \
-t /Users/hannah/Desktop/study/derivatives/fmriprep/sub-XXXX/ses-01/anat/sub-XXXX_ses-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5

Does anyone have any suggestions for going from subject space to freesurfer space (fsaverage surface space) without resampling? I see options for mri_vol2surf, but this resamples and not exactly what I would like to do.


I don’t understand how you hope to transform data into a different space without resampling. Could you clarify what you’re trying to do?