Hi all,
I am trying to replicate a step from the fmriprep pipeline by doing volume to surface resampling using mri_vol2surf,
I used the recommended flags :
mri_vol2surf --src <participant_ID>_task-ert_space-T1w_desc-preproc_bold.nii.gz --out lh.<participant_ID>_ert_fsaverage_T1w.mgh --regheader <participant_ID> --hemi lh --trgsubject fsaverage
However, compared the a surface output processed with fmriprep, <participant_ID>_task-ert_space-fsaverage_hemi-L.func.gii , the output from fmriprep appears to have a smoother surface.
Do you know why this may be the case? Is it because of averaging signal along the cortical ribbon? It appears that from the Fmriprep documentation : “For each vertex, the cortical ribbon is sampled at six points (spaced 20% of thickness apart) and averaged." Is there a way to replicate this using freesurfer’s mri_vol2surf?
I tried to add the flag --projfrac-avg 1.000 as seen in the Nypipe fs.SampleToSurface used by fmriprep but it doesn’t seem to work in my implementation, I get an error.
To summarize my question: how can I make the output obtained from mri_vol2surf outside of the fmriprep pipeline more similar to the one from fmriprep?
Below is what the output from fmriprep looks like and what I get using mri_vol2surf :
