Yes, I found it.

I should mention that, this log file is the result of today's preprocessing  (-projfrac 0.2) which I did in a separate folder, with all the previous preprocessing files being deleted.

As you see the -projfrac is still 0.5 !

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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Thursday, February 28, 2019 2:54:51 PM
To: 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.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
> N.,Ph.D. <DGREVE@mgh.harvard.edu>
> *Sent:* Thursday, February 28, 2019 2:41:25 PM
> *To:* 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
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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