THX for your response.
I have never move fs files. but i had a MATLAB 2011b, because of the virtual
machine`s 32 bit.
May this do harm? Or I don't configure the mat lab rightly?
here is the startup.m in ~/fsuser
%------------ FreeSurfer -----------------------------%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
%-----------------------------------------------------%
%------------ FreeSurfer FAST ------------------------%
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
%-----------------------------------------------------%
From: noahb.markow...@gmail.com
Date: Tue, 7 Jul 2015 13:15:19 +1000
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)
On the surface it seems like you moved the FS directory from one pathway to
another. If you place FS back into your applications folder, it may work. Also,
if you have Matlab 2014b or 2015a installed, it won’t work. You need
2012b-2014a for the process to run.
Hope this helps in any way.
Noah
On Jul 7, 2015, at 1:01 PM, jinyi <jiny...@hotmail.com> wrote:Hello Freesurfers
I meet a problem in calculate Lgi
I run fs in vituralBOX, matlab is installed. At the begining everything seems
fine .but error come in "make_outer_surface". The details are in below.
=========================================
xubuntu-VirtualBox:~> recon-all -s test001 -localGI
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxrwxrwx 1 fsuser fsuser 495621 Nov 17 2014
/usr/local/freesurfer/subjects/test001/scripts/recon-all.log
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14
UTC 2012 i686 i686 i386 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /Applications/freesurfer
/usr/local/freesurfer/subjects/test001/surf
#--------------------------------------------
#@# Local Gyrification Index lh Mon Jul 6 22:51:12 EDT 2015
mris_compute_lgi --i lh.pial
=================
rm -Rf /usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.0000
=================
make_outer_surface('/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=================
ERROR:: Too many arguments.
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