that is part of the bbregister command. Can you find the commands related to mri_vol2surf?
On 2/28/19 3:51 PM, Nasiriavanaki, Zahra wrote:
I did not find mri_vol2surf.
Below is part of a log file, as you see -projrfac has changed to 0.5 but not to 0.2.
mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg bold/020/tmp.bbregister.43919/reg.init.dat --out-reg bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR cd /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg bold/020/tmp.bbregister.43919/reg.init.dat --out-reg bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
Thanks
Mona
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Thursday, February 28, 2019 2:54:51 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] projfrac question
I would have thought that it would have changed. Can you look through the logs and find the mri_vol2surf command and verify that the --projfrac argument is changing?
On 2/28/19 2:51 PM, Nasiriavanaki, Zahra wrote:
Hi Doug
Thank you very much for your reply.
I was actually using -force and It did take a reasonable amount of time.
Then I ran the selxavg command to get the first level maps, and I guess It used the last preprocessd data which was from projfrac 0.2.
Thanks
Mona
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Thursday, February 28, 2019 2:41:25 PM *To:* freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] projfrac question The projfrac function might not be working in the way that you think. It might not actually be re-running anything. Did preproc-sess finish faster than you would have expected? You can try deleting the projfrac output and re-running. You can also run preproc-sess with -force, but this will force it to re-run everything. If you want to use multiple project fracs, then you should copy the functional tree to a new location (if you use -p with cp, it will copy the modification time, which will make preproc-sess run faster).
On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I was trying to look at the activation in different cortical layers in a _single subject_.
I ran my preproc-sess command three times, once without using -projfrac flag, once -projfrac 0.5 and lastly -projfrac 0.2
The activation patterns are exactly the same.
My voxel sizes are 1.1*1.1*1.1 .
My question is:
1-Is it normal that the activations do not change at all the more I get closer to white matter?
2-when I use -projfrac 0.2 , does it mean that I am averaging the activation between white matter layer to 0.2 of gray matter layer? Or is it averaging the activation between pial surface to 0.2 gray matter?
I hope my questions are clear.
Thanks
Mona
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