Hi Teresa
You should be able to load it as an overlay on the fsaverage4 subject. Note that you aren't converting the volume to a surface. Rather you are sampling it onto the surface. Have you run recon-all?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Tse, Teresa Sent: Saturday, July 18, 2020 6:32 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Converting volume to icosahedron surface
External Email - Use Caution Hi all,
I am trying to convert a volume file (fMRI data in nifti format) into an icosahedron (4th order) surface using Freesurfer's mri_vol2surf command. I have been using nipype as a wrapper for Freesurfer and the other packages that I need for my processing. The command that nipype ran is:
mri_vol2surf --hemi lh --icoorder 4 --o /dev/shm/RT_processing/_hemi_lh/to_surface/lh.003-FunctionalCMRR-2mm69sl1p5s_mcf.mgz --reg /dev/shm/RT_processing/convert_xfm/InplanetoAnatomy.xfm --projfrac-avg 0.000 1.000 0.100 --mov /dev/shm/RT_processing/motion_correction/003-FunctionalCMRR-2mm69sl1p5s_mcf.nii.gz --trgsubject ico
The output of this command is a mgz file (attached to this email). I was unable to view this mgz file using Freeview's "Load surface" (I get the error "freadFloat: fread failed"). I was able to load the mgz file into Matlab using the load_mgh function. It loaded as a 2562 length vector (consistent with the number of vertices of a ico-4 surface). I have several questions regarding the output of the mri_vol2surf command that was run.
1) I am unsure as to whether the command that was used is correct, and whether the output mgz file that I got is the correct or expected output. What do the values of the vector represent? 2) Do you know how to load and view the output mgz file in Freeview? Is it supposed to be an overlay or annotation to an ico-4 surface file? If so, where would I find this ico-4 surface? 3) How do I find documentation and information about the icosahedron surface in Freesurfer?
Many thanks, Teresa