Can you try it again? this time use -projfrac 0.2 pf020  (ie, add
"pf020" after 0.2). Then when you use mkanalysis-sesss, add -expkey
pf020 to the command line. The pf020 will be included in the output file
name to make it unique. This allows you to use a single project folder
(ie, you don't need to copy to a new folder).

On 3/7/19 12:20 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I ran one of my subjects with the command below and I got this error:
>
> preproc-sess.test -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2
> -surface fsaverage lhrh -fsd bold -d $dir/all_subjects -force
>
> Does it mean I should run it with expert option flag?like the one in
> recon-all?
>
>
> Thu Mar  7 10:10:00 EST 2019
> mc-sess completed SUCCESSFULLY
> inul_reunpack To Surface -----------------------------
> rawfunc2surf-sess -fwhm 0 -s inul_reunpack -d
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects -fsd bold
> -trgsubject fsaverage -per-run -projfrac 0.2
> ERROR: experts key needed (-expkey)
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> ------------------------------------------------------------------------
> *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:* Wednesday, March 6, 2019 7:06:44 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
> This does appear to be a bug. Are you using FS version 6? If so, I put a
> test in that distriubtion called preproc-sess.test. Can you try running
> that on a subject and see if you get the desired behavior?
>
> On 3/6/19 1:31 PM, Nasiriavanaki, Zahra wrote:
> >
> > Hi Doug
> >
> >
> > I re-analyzed one of my subjects from the very beginning with
> > -projfrac 0.2. But still, in mri_vol2surf, the projfrac is 0.5 (copied
> > below). Could you please let me know what I'm doing wrong?
> >
> > Here is my command:
> >
> > preproc-sess -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface
> > fsaverage lhrh -fsd bold -d $dir/all_subjects -force
> >
> >
> > Thanks
> >
> > Mona
> >
> >
> > mri_vol2surf --mov
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> > --reg
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> > --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> > --noreshape --cortex --surfreg sphere.reg
> > srcvol =
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> > srcreg =
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = rh
> > trgsubject = fsaverage
> > surfreg = sphere.reg
> > ProjFrac = 0.5
> > thickness = thickness
> > reshape = 0
> > interp = trilin
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > Done loading volume
> > Input reg is LTA
> >
> >
> >
> > *Zahra (Mona) Nasiriavanaki*
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> > ------------------------------------------------------------------------
> > *From:* Nasiriavanaki, Zahra
> > *Sent:* Friday, March 1, 2019 11:52:21 AM
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] projfrac question
> >
> > 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 !
> >
> >
> >   Fri Mar  1 11:32:16 EST 2019
> > mri_vol2surf --mov
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
> > --reg
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> > --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> > --noreshape --cortex --surfreg sphere.reg
> > srcvol =
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
> > srcreg =
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = rh
> > trgsubject = fsaverage
> > surfreg = sphere.reg
> > ProjFrac = 0.5
> > thickness = thickness
> > reshape = 0
> > interp = trilin
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > Done loading volume
> > Input reg is LTA
> >
> >
> > ------------------------------------------------------------------------
> > *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:* Friday, March 1, 2019 11:09:30 AM
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] projfrac question
> > 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.edu
> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> >> <freesurfer-bounces@nmr.mgh.harvard.edu>
> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve,
> >> Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu>
> >> *Sent:* Thursday, February 28, 2019 2:54:51 PM
> >> *To:* freesurfer@nmr.mgh.harvard.edu
> >> <mailto: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
> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> >> > <freesurfer-bounces@nmr.mgh.harvard.edu>
> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve,
> >> Douglas
> >> > N.,Ph.D. <DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu>
> >> > *Sent:* Thursday, February 28, 2019 2:41:25 PM
> >> > *To:* freesurfer@nmr.mgh.harvard.edu
> >> <mailto: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
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> Freesurfer Info Page - Harvard University
> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >> mail.nmr.mgh.harvard.edu
> >> To see the collection of prior postings to the list, visit the
> >> Freesurfer Archives.. A searchable archive which of messages PRIOR to
> >> March 2004 is at this site A searchable archive which includes
> >> messages AFTER March 2004 is at this site. Using Freesurfer
> >>
> >>
> >>
> >> >
> >> >
> >> > _______________________________________________
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> >> >
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> >>
> >>
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> >>
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> >
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