You can see that it is running matlab just before the error. So it must be using the matlab load_mgh function, which does convert from mgz to mgh and then deletes the tmp file when it is done. Maybe you are setting rm as an alias for 'rm -i' in your .cshrc.
Subject: Re: [Freesurfer] LGI From: nicks@nmr.mgh.harvard.edu To: leila.cammoun@epfl.ch Date: Tue, 15 Apr 2008 13:04:13 -0400 CC: freesurfer@nmr.mgh.harvard.edu
Leila,
This is a strange error. The LGI utility doesnt work with .mgh files (it uses .mgz), so I am not sure where or how the 'rm: remove regular file `/tmp/tmp8147237.mgh'? ' message originates.
I would try deleting all the .mgh files in the /tmp directory, and try again. And if the message repeats, try using mri_info on the file to determine its origin. Or you can try responding with 'y' to the prompt and see if it continues.
Nick
On Tue, 2008-04-15 at 18:29 +0200, Leila BH wrote:
Hi
I am trying to launch the LGI option, but the program seems to wait for a response, here is the complete output,. Even if I type yes it doesn’t seems to continue.
Do you know how to solve this?
Thanks in advance
Leila
[cammoun@lts1pc72 ~/freesurfer]# recon-all -lgi -sid chuv60
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /home/cammoun/freesurfer
-rwxrwxrwx 1 root root 569567 Apr 15 18:20 /usr/local/freesurfer/subjects/chuv60/scripts/recon-all.log
Linux lts1pc72.epfl.ch 2.6.20-1.2944.fc6 #1 SMP Tue Apr 10 17:46:00 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /home/cammoun/freesurfer Previous: /usr/local/freesurfer/usr/local/freesurfer/subjects/chuv60/surf
#--------------------------------------------
#@# Local Gyrification Index lh Tue Apr 15 18:21:04 CEST 2008
mris_compute_lgi --i lh.pial
=================
rm -Rf tmp-mris_compute_lgi
=================
=================
mkdir -p tmp-mris_compute_lgi
=================
=================
mris_fill -c -r 1 lh.pial tmp-mris_compute_lgi/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to tmp-mris_compute_lgi/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.0000
=================
make_outer_surface('tmp-mris_compute_lgi/lh.pial.filled.mgz',15,'tmp- mris_compute_lgi/lh.pial-outer')
=================
Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.5.0.338 (R2007b) August 9, 2007To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
reading filled volume...
rm: remove regular file `/tmp/tmp8147237.mgh'?
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