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
*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
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
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