Hi FS Forum,

I am following up on this post because after using mri_vol2surf to downsample my scans to fsaverage4, I ended up with empty files when viewed in Freeview. This is the command that I ran generally:

mri_vol2surf --src bold_preproc.nii.gz --out lh.imagename.nii.gz --regheader sub-01 --trgsubject fsaverage4 -hemi lh

I am assuming there are some tags that I may be missing which are leading me to output with empty nii.gz files. The input bold preprocessed files are viewed normally in Freeview, but the output is empty.

Thank you in advance.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, March 18, 2021 9:43 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] fMRIPrep BOLD Output

sounds like you need mri_vol2surf (use --projfrac 0.5)

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Hi Freesurfer List,

I am running fMRIPrep and getting the first two FS output files (aseg and aparcaseg seen above in the screenshot), but not the actual file I need which is the one where it is resampled to the mesh. I have run fMRIPrep and have those two files except the actual BOLD series resampled to the surface mesh. Is there a FS command that can be used to do that one step?

Best,

Karan

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