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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