Hi Elisa,
Thanks for the update, does that mean that just adding -f to all rm in load_mgh.m worked for you? Sounds great, thanks for keeping us posted! Indeed, it's not that nobody computed the lGI, lots of people used it in published studies and from what I see in the mailing list, and I definitely used it on tons of different computer configurations, and only in one case I got this error message. It was on a lab unix server shared between many people where the rm command was aliased to copy files to the recycle bin. Not having access to this rm parameters, even using the rm -f didn't solve the problem. So, it's definitely not an lGI issue, but a rm issue…
Hope everything else will go well with your processing,
Marie
On Jul 3, 2014, at 2:59 AM, elisa veronese <dovreipensarci@gmail.commailto:dovreipensarci@gmail.com> wrote:
YEAH! Now it is working, the '-f' option is doing something! Actually it is still in progress, I do not know if it's going to work properly until the end. But at least something is happening :)
Thank you, Marie! (Did you add the '-f' to all the rm in load_mgh.m?)
Best,
Elisa
2014-07-03 11:46 GMT+02:00 elisa veronese <dovreipensarci@gmail.commailto:dovreipensarci@gmail.com>: Dear Marie,
thank fot your email. I'm quite confused, it seems like nobody has ever computed this localGI :(
Yes, before writing to the FS mailing list i checked in the internet if anybody had had my problem and I found your posts. I will try adding the -f to force the removal, it could be an idea. I'll let you know.
Ehm... what do you mean by "to process the LGI on another computer"? Do you think it is a problem linked to the OS?
Best,
Elisa
2014-07-02 19:17 GMT+02:00 Marie Schaer <Marie.Schaer@unige.chmailto:Marie.Schaer@unige.ch>:
Hello Elisa,
I've seen this issue that the process gets stuck even if you answer the question. That happened to me and others before, see the following posts:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg07251.html
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32912.html
But I'm afraid that we didn't find the full solution to this yet. We tried replacing all the "rm" by "rm -f" in load_mgh.m, but it didnt help. Can you try that? Maybe you're more lucky than me. So finally, on my side, the only solution I found was to process the LGI on another computer… but it's definitely not ideal!
Otherwise, maybe someone else has solved this issue without posting the reply on the mailing list. If yes, I'd be very grateful to know the answer, thanks in advance!
Best,
Marie
On Jul 2, 2014, at 12:13 AM, elisa veronese <dovreipensarci@gmail.commailto:dovreipensarci@gmail.com> wrote:
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. 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. Best 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 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/freesurferhttp://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.comhttp://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.edumailto:greve@nmr.mgh.harvard.edu>:
#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:
- 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/freesurferhttp://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, 2012To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.comhttp://www.mathworks.com/ <http://www.mathworks.comhttp://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.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358tel:617-724-2358 Fax: 617-726-7422tel:617-726-7422
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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, Italy ICBN 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- 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
-- 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
Hi all, I had an error message while running LGI recon I am using Freesurfer 5.3 with a MacOS lion 10.7.5 and Matlab 2013b with the Image processing toolbox
Any help is welcome. Thank you! Angela
the error is:
mesh_outer =
vertices: [61278x3 double] faces: [122552x3 double] facesOfVertex: [61278x1 struct]
preparing pial mesh structure ... ...searching for mesh edges...done (315.30 sec). ... creating path file for vertex 1 / 61278 area file for outer ROIs saved at 1 {Improper assignment with rectangular empty matrix.
Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2));
Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points);
Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); }
ERROR: make_roi_paths did not complete successfully! Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
recon-all -s subj001 exited with ERRORS at Tue Jul 15 10:23:17 CEST 2014
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
angela.favaro＠unipd.it -
Marie Schaer