elisaBestThank you.Now my tmp folder contains just one file (edit.dat). Below you can see what I see from my terminal. The terminal has been stuck there since yesterday.Thank you Doug,anyway I'm afraid I still have problems with the recon-all -localGI. After answering yes to the removal of the temporary file, it seems that the program stops without doing anything.
[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 1658172 Jul 1 17:30 /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
/root/Desktop/fselisa/1379341346/surf
#--------------------------------------------
#@# Local Gyrification Index lh Tue Jul 1 17:31:13 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.
>> reading filled volume...
rm: remove regular file `/tmp/tp1773697773286350.load_mgh.2127429.mgh'? y
_______________________________________________
2014-06-27 20:25 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>:
#1. not a problem
#2. yes, delete it
doug
> 1. should I worry about the /Warning: Unable to open display
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:
> 'iconic'. You will not be able to display graphics on the screen. /?/
> /> answering /no/, but now everything seems to be stuck without
> 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
> performing any subsequent processing.> <http://6004023.clrlcgce03.in2p3.fr/CREAM251988513/DIRAC_lhrUhWpilot/6418014/recon-all.sh-3038867747447129/freesurfer>
>
> 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://www.mathworks.com>.> /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
>> /
> >> 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
> /
>
> /
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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--
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, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php
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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 Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.