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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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:
External Email - Use Caution
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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