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.edu> wrote:
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
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>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
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>
>     --
>     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>
>
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>
>
>     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
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--
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

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