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
>
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