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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. <dgr...@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-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu> >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, >> Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> <mailto:dgr...@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-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> > <freesurfer-boun...@nmr.mgh.harvard.edu> >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, >> Douglas >> > N.,Ph.D. <dgr...@mgh.harvard.edu> <mailto:dgr...@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 >> >> >> >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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