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, 2007

To 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'?

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_________________________________________________________________ Pack up or back up–use SkyDrive to transfer files or keep extra copies. Learn how. http://www.windowslive.com/skydrive/overview.html?ocid=TXT_TAGLM_WL_Refresh_...