How often does it happen? Does the process just hang or does it produce the correct results (eventually)? I don't think it is related to load_mgh.m because the temporary filename would be different. However, it is consistent with the temp files used with nifti reading and writing. Does that happen in the lGI stream? doug
On 12/06/2013 01:46 PM, Marie Schaer wrote: > > Hi Kangchen, > > I also had the same error recently on a unix machine, but I > unfortunately did not find the solution and some help would be greatly > appreciated. > > I think that the bug is due to the fact that make_outer_surface.m > calls MRIread.m, which calls load_mgh.m and that something gets wrong > at the point of reading the file (and removing temporary files). But > I'm afraid I can't help more, I tried to edit load_mgh to add -f after > rm and it didn't help. > > Nick or Doug, any idea? > > Many thanks in advance! > > Marie > > On Dec 6, 2013, at 5:31 AM, 王康程 <kangchengwang0...@gmail.com > <mailto:kangchengwang0...@gmail.com>> wrote: > >> Dear all， >> >> When I run "recon-all -s ${subject} -localGI", it appear "rm: remove >> regular file `/tmp/tmp4653077.mgh'? ". Then, I write yes, however, it >> didn't response anyway. How shold I do next? Thank you! >> >> The echo for the process is followed >> >> -------------------------- >> running subject Emotion_xunlian_s12002 >> -------------------------- >> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> INFO: SUBJECTS_DIR is /home/fmri/desktop/test >> Actual FREESURFER_HOME /usr/local/freesurfer >> -rw-rw-r--. 1 root root 544815 Dec 6 20:54 >> /home/fmri/desktop/test/Emotion_xunlian_s12002/scripts/recon-all.log >> Linux localhost.localdomain 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct >> 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux >> /home/fmri/desktop/test/Emotion_xunlian_s12002/surf >> #-------------------------------------------- >> #@# Local Gyrification Index lh Fri Dec 6 21:07:40 CST 2013 >> >> mris_compute_lgi --i lh.pial >> >> ================= >> rm -Rf >> /home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial >> ================= >> ================= >> mkdir -p >> /home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial >> ================= >> ================= >> mris_fill -c -r 1 lh.pial >> /home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz >> ================= >> reading surface from lh.pial... >> writing filled volume to >> /home/fmri/desktop/test/Emotion_xunlian_s12002/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('/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/fmri/desktop/test/Emotion_xunlian_s12002/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. >> R2012a (7.14.0.739) 64-bit (glnxa64) >> February 9, 2012 >> >> Toolbox Path Cache read in 0.02 seconds. >> MATLAB Path initialized in 0.79 seconds. >> >> 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... >> -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /usr/local/freesurfer >> FSFAST_HOME /usr/local/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /home/fmri/desktop/test >> MNI_DIR /usr/local/freesurfer/mni >> FSL_DIR /opt/fsl >> -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /usr/local/freesurfer >> FSFAST_HOME /usr/local/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /home/fmri/desktop/test >> MNI_DIR /usr/local/freesurfer/mni >> FSL_DIR /opt/fsl >> rm: remove regular file `/tmp/tmp4653077.mgh'? >> >> -- >> kangcheng Wang >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > _______________________________________________ > 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 gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
