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 /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.
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reading filled volume...
rm: remove regular file `/tmp/tp726715349117711.load_mgh.8128471.mgh'?