Re: [Freesurfer] projfrac question
Dear Doug Thank you so very much for your time and helps. Yes It works perfectly. Mona From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, March 7, 2019 6:07:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] projfrac question 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-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *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. > > > >
Re: [Freesurfer] projfrac question
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-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *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/7
Re: [Freesurfer] projfrac question
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 on behalf of Greve, Douglas N.,Ph.D. 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 > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Friday, March 1, 2019 11:09:30 AM > *To:* freesurfe
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 > on behalf of Greve, Douglas > N.,Ph.D. > *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_lo
Re: [Freesurfer] projfrac question
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 on behalf of Greve, Douglas N.,Ph.D. 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> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <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
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 on behalf of Greve, Douglas N.,Ph.D. 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> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <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> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Greve, Douglas > N.,Ph.D. <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
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> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <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> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Greve, Douglas > N.,Ph.D. <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 > Frees
Re: [Freesurfer] projfrac question
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 on behalf of Greve, Douglas N.,Ph.D. 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-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *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 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 > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 > on behalf of Greve, Douglas > N.,Ph.D. > *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 > > > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] projfrac question
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 on behalf of Greve, Douglas N.,Ph.D. 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 ___ 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
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
