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 <kangchengwang0808@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.

>> 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
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