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 <gr...@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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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. > >
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