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.
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