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
%--------------------------------------------------------------------------------------------------------------------------------------------
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