#1. not a problem
#2. yes, delete it

doug

On 06/27/2014 03:41 AM, elisa veronese wrote:
> Dear FS users,
>
> I'm trying the -localGI on a linux Centos machine, but I'm facing some
> problems:

> 1. should I worry about the /Warning: Unable to open display
> 'iconic'.  You will not be able to display graphics on the screen. /?/

> /
> 2. the script asks me if I wan to remove a file (rm: remove regular
> file `/tmp/tp726715349117711.load_mgh.8128471.mgh'?).  Should I say
> yes and remove it? Is it important? Should I keep it? I tried

> answering /no/, but now everything seems to be stuck without

> performing any subsequent processing.
>
> Below there is the output I got.
>
> Thank you.
> Regards,
> elisa
>
>
> [root@gc02lx fselisa]# recon-all -s 1379341346/ -sd
> /root/Desktop/fselisa/ -localGI
> INFO: FreeSurfer build stamps do not match
> Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /root/Desktop/fselisa
> Actual FREESURFER_HOME /usr/local/freesurfer
> -rw-r--r--. 1 root root 1624545 Jun 26 18:08
> /root/Desktop/fselisa/1379341346/scripts/recon-all.log
> Linux gc02lx 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT
> 2013 x86_64 x86_64 x86_64 GNU/Linux
> INFO: current FREESURFER_HOME does not match that of previous processing.
>     Current: /usr/local/freesurfer
>     Previous:
> /home/tmp/6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014/recon-all.sh-3038867747447129/freesurfer

> <http://6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014/recon-all.sh-3038867747447129/freesurfer>

> /root/Desktop/fselisa/1379341346/surf
> #--------------------------------------------
> #@# Local Gyrification Index lh Fri Jun 27 09:23:34 CEST 2014
>
>  mris_compute_lgi --i lh.pial
>
> =================
> rm -Rf /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial
> =================
> =================
> mkdir -p
> /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial
> =================
> =================
> mris_fill -c -r 1 lh.pial
> /root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
> =================
> reading surface from lh.pial...
> writing filled volume to
> /root/Desktop/fselisa/1379341346/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('/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/root/Desktop/fselisa/1379341346/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
> exit
> =================
> Warning: Unable to open display 'iconic'.  You will not be able to
> display graphics on the screen.
>
>                             < M A T L A B (R) >
>                   Copyright 1984-2012 The MathWorks, Inc.
>                     R2012b (8.0.0.783) 64-bit (glnxa64)
>                               August 22, 2012
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com

> <http://www.mathworks.com>.

>
> >> reading filled volume...
> rm: remove regular file `/tmp/tp726715349117711.load_mgh.8128471.mgh'?
>
>
>
> --
> Elisa Veronese - PhD
>
> /
> Research Unit on Brain Imaging and Neuropsychology (RUBIN)

> /

> /
> Inter-University Center for Behavioral Neurosciences (ICBN)
> University of Udine and University of Verona, Italy

> /
> ICBN Website: http://icbn.uniud.it/tiki-index.php
> /
>
> /
>
>
> _______________________________________________
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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
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