Re: [Freesurfer] preproc-sess error in version 5.0 - Freesurfer

9 Dec 2010

      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
>

%--------------------------------------------------------------------------------------------------------------------------------------------
    >
    >
    ------------------------------------------------------------------------
    >
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--
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

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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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-- 
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
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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
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