Re: [Freesurfer] Resting state fMRI - volume analysis

Did you see the part about only analyzing subcortical gray matter earlier in our conversation?

On 10/7/2020 12:00 PM, Wenzhen Zhao wrote:

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Hi,

I find it weird that it does not show full brain after smoothing (-fwhm 5). Is this normal?

Also, even with -no-subcort-mask, volume analysis does not do full brain analysis.

Best, Wenzhen

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

...

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*From:*freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu><freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of
Wenzhen Zhao <wenzhen.zhao@yale.edu <mailto:wenzhen.zhao@yale.edu>>
*Sent:*Monday, October 5, 2020 3:22 PM
*To:*Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto: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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