Correct, we analyze the cortical surface using surface-based analysis. If you want to have full volume analysis, you can add -no-subcort-mask to preproc-sess. Not sure what the problem is with smoothing.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wenzhen Zhao <wenzhen.zhao@yale.edu>
Sent: Monday, October 5, 2020 3:22 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Resting state fMRI - volume analysis
 

        External Email - Use Caution        

Dear Freesurfer Developers, 

I have a question regarding volume analysis of fMRI data. I wanted to perform volume analysis in MNI305 space, and I used following command after creating a seed; 

$mkanalysis-sess -analysis lh.pcc.mni305.vol -mni305 2 -stc siemens -fwhm 0 -notask -taskreg lh.pcc.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 10 -fsd rest -hpf 0.01 -TR 3 -per-run

$selxavg3-sess -s sess01 -a lh.pcc.mni305.vol -no-preproc -overwrite

The resulting analysis seems only showing subcortical regions, not the whole brain. (Shown in the attachment) I read on the page that volume analysis is only for subcortical regions, is this the reason that I only see subcortical regions?

Another problem is that in the preprocessing step, I could not smooth the volume. If I do, it seems to distort the image and only gives something similar to the picture shown. Could this be the reason for the distorted analysis? 

Thanks for your help. 

Best, 
Wenzhen