OK, I've tracked down and fixed the error. You can get a new version from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist
let me know if that works. doug Katherine Sledge Moore wrote: > Hi, > > I was wondering whether there was any progress on this issue (copied > below)? I have had the same experience as "yuko YY," except that I do > not have access to version 4.5 so I never installed a version of > getrunlist that worked for me. > > To recap, when I try to run a preprocess session, I get output similar > to yuko's. The same is true of "getrunlist." But I can cd into the > folder where my bold runs are, of course. And when I run "find . > -maxdepth 1 -name "[0-9][0-9][0-9]" I get a list of my runs for that > directory (as did yuko). My file structure is essentially the same as > yuko's. > > --Katherine > > 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 > > <gr...@nmr.mgh.harvard.edu <mailto: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 <mailto: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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 > <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 > > > Katherine Sledge Moore > Postdoctoral Associate > Visual Cognitive Neuroscience Laboratory > Yale University > http://camplab.psych.yale.edu/ > http://pantheon.yale.edu/~khs8 <http://pantheon.yale.edu/%7Ekhs8> > -- 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
