Did you check that the bold is really in register with the anat? You can do this with tkregisterfv --mov bold_preproc.nii.gz --s sub-01--reg deleteme.lta --surfs
On 3/31/2021 10:49 AM, Karan Desai wrote:
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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--srcbold_preproc.nii.gz --outlh.imagename.nii.gz--regheadersub-01--trgsubject fsaverage4 -hemilh
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)
On 3/18/2021 11:38 AM, Karan Desai wrote:
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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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