Hello,
I recently switch to version 5, and am having a problem with preproc-sess in version 5.0. version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 OS : Mac 10.6.5
When I ran: preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold
I got the following error: %-------------------------------------------------------------------------------------------------------------------------------------------- [Yukos-iMac:sessions/VM/VMan] yuko% preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ yuko setenv FREESURFER_HOME /Applications/freesurfer/freesurfer setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/freesurfer/fsfast/bin/preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold Tue Nov 23 19:46:29 JST 2010 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain VM20 Template ----------------------------- mktemplate-sess -s VM20 -d /Users/yuko/Documents/FreeSurfer/sessions/VM -fsd bold
Session: /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 ---------------- Tue Nov 23 19:46:29 JST 2010 find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found %--------------------------------------------------------------------------------------------------------------------------------------------
I found the same error reported in msg14982, but couldn't find a solution. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14982.html
Can anyone tell me what I need to do to make this work? Yuko Yotsumoto
% additional info -------------------------------------------------------------------------------------------------------------------------------------------- My data are at: sessions/VM/VM20/bold/001/f.nii sessions/VM/VM20/bold/002/f.nii .. sessions/VM/VM20/bold/009/f.nii
and my study directory is at: sessions/VM/VMan/
subject is at: subjects/VM20 %--------------------------------------------------------------------------------------------------------------------------------------------
Hi Yuko, can you try running:
getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold
If that fails, try this:
cd /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold
doug
yuko YY wrote:
Hello,
I recently switch to version 5, and am having a problem with preproc-sess in version 5.0. version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 OS : Mac 10.6.5
When I ran: preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold
I got the following error: %-------------------------------------------------------------------------------------------------------------------------------------------- [Yukos-iMac:sessions/VM/VMan] yuko% preproc-sess -per-session -fwhm 5
-force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold
preproc-sess logfile is log/preproc-sess.log
$Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ yuko setenv FREESURFER_HOME /Applications/freesurfer/freesurfer setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/freesurfer/fsfast/bin/preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold Tue Nov 23 19:46:29 JST 2010 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain VM20 Template ----------------------------- mktemplate-sess -s VM20 -d /Users/yuko/Documents/FreeSurfer/sessions/VM -fsd bold
Session: /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20
Tue Nov 23 19:46:29 JST 2010 find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found %--------------------------------------------------------------------------------------------------------------------------------------------
I found the same error reported in msg14982, but couldn't find a solution. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14982.html
Can anyone tell me what I need to do to make this work? Yuko Yotsumoto
% additional info
My data are at: sessions/VM/VM20/bold/001/f.nii sessions/VM/VM20/bold/002/f.nii .. sessions/VM/VM20/bold/009/f.nii
and my study directory is at: sessions/VM/VMan/
subject is at: subjects/VM20 %--------------------------------------------------------------------------------------------------------------------------------------------
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
"getrunlist /Users/yuko/.../bold" failed, and cd to bold didn't work either (error message pasted below). Then, Mark suggested me to replace /fsfast/bin/getrunlist with the one from v4.5.0., which solved the problem.
Thank you Doug & Mark! Yuko Yotsumoto
%------- getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM00/bold/ find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found %--------
On Wed, Nov 24, 2010 at 1:29 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Yuko, can you try running:
getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold
If that fails, try this:
cd /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold
doug
yuko YY wrote:
Hello,
I recently switch to version 5, and am having a problem with preproc-sess in version 5.0. version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 OS : Mac 10.6.5
When I ran: preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold
I got the following error:
%--------------------------------------------------------------------------------------------------------------------------------------------
[Yukos-iMac:sessions/VM/VMan] yuko% preproc-sess -per-session -fwhm 5
-force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold
preproc-sess logfile is log/preproc-sess.log
$Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ yuko setenv FREESURFER_HOME /Applications/freesurfer/freesurfer setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/freesurfer/fsfast/bin/preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold Tue Nov 23 19:46:29 JST 2010 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain VM20 Template ----------------------------- mktemplate-sess -s VM20 -d /Users/yuko/Documents/FreeSurfer/sessions/VM -fsd bold
Session: /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20
Tue Nov 23 19:46:29 JST 2010 find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found
%--------------------------------------------------------------------------------------------------------------------------------------------
I found the same error reported in msg14982, but couldn't find a
solution.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14982.html
Can anyone tell me what I need to do to make this work? Yuko Yotsumoto
% additional info
My data are at: sessions/VM/VM20/bold/001/f.nii sessions/VM/VM20/bold/002/f.nii .. sessions/VM/VM20/bold/009/f.nii
and my study directory is at: sessions/VM/VMan/
subject is at: subjects/VM20
%--------------------------------------------------------------------------------------------------------------------------------------------
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Yes, that will solve the problem, I just don't know why it's a problem to start with. If you cd into that bold dir, can you run:
find . -maxdepth 1 -name "[0-9][0-9][0-9]"
doug
yuko YY wrote:
Hi Doug,
"getrunlist /Users/yuko/.../bold" failed, and cd to bold didn't work either (error message pasted below). Then, Mark suggested me to replace /fsfast/bin/getrunlist with the one from v4.5.0., which solved the problem.
Thank you Doug & Mark! Yuko Yotsumoto
%------- getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM00/bold/ find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found %--------
On Wed, Nov 24, 2010 at 1:29 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yuko, can you try running: getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold If that fails, try this: cd /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold doug yuko YY wrote: > Hello, > > I recently switch to version 5, and am having a problem with > preproc-sess in version 5.0. > version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 > OS : Mac 10.6.5 > > When I ran: > preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df > sessdirfile -s VM20 -fsd bold > > I got the following error: > %-------------------------------------------------------------------------------------------------------------------------------------------- > [Yukos-iMac:sessions/VM/VMan] yuko% preproc-sess -per-session -fwhm 5 > -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold > -------------------------------------------------------------- > preproc-sess logfile is log/preproc-sess.log > -------------------------------------------------------------- > $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ > yuko > setenv FREESURFER_HOME /Applications/freesurfer/freesurfer > setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects > Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov > 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 > /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan > /Applications/freesurfer/freesurfer/fsfast/bin/preproc-sess > -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 > -fsd bold > Tue Nov 23 19:46:29 JST 2010 > instem f > mc 1 f fmcpr > stc 0 fmcpr > sm 0 > mask 1 brain > VM20 Template ----------------------------- > mktemplate-sess -s VM20 -d > /Users/yuko/Documents/FreeSurfer/sessions/VM -fsd bold > > Session: /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 > ---------------- > Tue Nov 23 19:46:29 JST 2010 > find: illegal option -- m > find: illegal option -- a > find: illegal option -- e > find: illegal option -- p > find: illegal option -- t > find: illegal option -- h > find: 1: No such file or directory > ERROR: no run directories found > %-------------------------------------------------------------------------------------------------------------------------------------------- > > I found the same error reported in msg14982, but couldn't find a solution. > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14982.html > > Can anyone tell me what I need to do to make this work? > Yuko Yotsumoto > > > % additional info > -------------------------------------------------------------------------------------------------------------------------------------------- > My data are at: > sessions/VM/VM20/bold/001/f.nii > sessions/VM/VM20/bold/002/f.nii > .. > sessions/VM/VM20/bold/009/f.nii > > and my study directory is at: > sessions/VM/VMan/ > > subject is at: > subjects/VM20 > %-------------------------------------------------------------------------------------------------------------------------------------------- > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
at /Yukos-iMac:VM/VM00/bold find . -maxdepth 1 -name "[0-9][0-9][0-9]" gave ./001 ./002 ./003
at /Yukos-iMac:VM/VM00/bold/001 find . -maxdepth 1 -name "[0-9][0-9][0-9]" output nothing.
Yuko
On Thu, Nov 25, 2010 at 4:17 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Yes, that will solve the problem, I just don't know why it's a problem to start with. If you cd into that bold dir, can you run:
find . -maxdepth 1 -name "[0-9][0-9][0-9]"
doug
yuko YY wrote:
Hi Doug,
"getrunlist /Users/yuko/.../bold" failed, and cd to bold didn't work either (error message pasted below). Then, Mark suggested me to replace /fsfast/bin/getrunlist with the one from v4.5.0., which solved the problem.
Thank you Doug & Mark! Yuko Yotsumoto
%------- getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM00/bold/ find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found %--------
On Wed, Nov 24, 2010 at 1:29 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Yuko, can you try running: getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold If that fails, try this: cd /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold doug yuko YY wrote: > Hello, > > I recently switch to version 5, and am having a problem with > preproc-sess in version 5.0. > version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 > OS : Mac 10.6.5 > > When I ran: > preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df > sessdirfile -s VM20 -fsd bold > > I got the following error: >%--------------------------------------------------------------------------------------------------------------------------------------------
> [Yukos-iMac:sessions/VM/VMan] yuko% preproc-sess -per-session -fwhm 5 > -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold > -------------------------------------------------------------- > preproc-sess logfile is log/preproc-sess.log > -------------------------------------------------------------- > $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ > yuko > setenv FREESURFER_HOME /Applications/freesurfer/freesurfer > setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects > Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: FriNov
> 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 > /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan > /Applications/freesurfer/freesurfer/fsfast/bin/preproc-sess > -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 > -fsd bold > Tue Nov 23 19:46:29 JST 2010 > instem f > mc 1 f fmcpr > stc 0 fmcpr > sm 0 > mask 1 brain > VM20 Template ----------------------------- > mktemplate-sess -s VM20 -d > /Users/yuko/Documents/FreeSurfer/sessions/VM -fsd bold > > Session: /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 > ---------------- > Tue Nov 23 19:46:29 JST 2010 > find: illegal option -- m > find: illegal option -- a > find: illegal option -- e > find: illegal option -- p > find: illegal option -- t > find: illegal option -- h > find: 1: No such file or directory > ERROR: no run directories found >%--------------------------------------------------------------------------------------------------------------------------------------------
> > I found the same error reported in msg14982, but couldn't find a solution. >http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14982.html
> > Can anyone tell me what I need to do to make this work? > Yuko Yotsumoto > > > % additional info >
> My data are at: > sessions/VM/VM20/bold/001/f.nii > sessions/VM/VM20/bold/002/f.nii > .. > sessions/VM/VM20/bold/009/f.nii > > and my study directory is at: > sessions/VM/VMan/ > > subject is at: > subjects/VM20 >%--------------------------------------------------------------------------------------------------------------------------------------------
> >
> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
yuko YY