On Wed, Oct 7, 2020 at 10:16 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

What is wrong?
On 10/6/2020 12:28 PM, Wenzhen Zhao wrote:
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Thank you for your help.

The smoothing issue occurs only on volume. It works okay with surface. When I smooth the volume by 5, the results look like below. The command I used was $preproc-sess -s sess01 -fsd rest -stc siemens -noreg -mni305 -vol-fwhm 5 -no-subcort-mask -per-run -update

Thanks,

Wenzhen

On Oct 6, 2020, at 11:53 AM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

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

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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

<Screen Shot 2020-10-05 at 2.31.29 PM.png>

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