Dear all,
I am trying to compute the local gyrification index but unfortunately encounter
the problem below. Matlab Version (7.7.0.471 - R2008b) and also the Image
Processing Toolbox are installed on my computer.
As I understand 'make_outer_surface' does not find
'tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz'. However when checking the
surf directory I can see that
tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz exists. So maybe it is just
a path problem?
Any help is greatly appreciated!
Best wishes,
Christian Scheel
---
Here is the output:
[r...@localhost christian]$ recon-all -s bert -localGI
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0
INFO: SUBJECTS_DIR is /home/freesurfer/christian
Actual FREESURFER_HOME /usr/local/freesurfer_410
-rw-rw-r-- 1 freesurfer freesurfer 906671 Jan 20 14:30
/home/freesurfer/christian/bert/scripts/recon-all.log
Linux localhost.localdomain 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007
i686 i686 i386 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer_410
Previous: /space/freesurfer/build/pub-releases/freesurfer
/home/freesurfer/christian/bert/surf
#--------------------------------------------
#...@# Local Gyrification Index lh Tue Jan 20 14:43:39 CET 2009
mris_compute_lgi --i lh.pial
=================
rm -Rf tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.0000
=================
make_outer_surface('tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=================
----------------------------------------------------------------------------
Warning: glibc 2.3.4 - Your version
glibc 2.3.6 - MATLAB built using this version
----------------------------------------------------------------------------
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 1984-2008 The MathWorks, Inc.
Version 7.7.0.471 (R2008b)
September 17, 2008
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> reading filled volume...
zcat: tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz: No such file or
directory
ERROR: problem reading fname
??? SWITCH expression must be a scalar or string constant.
Error in ==> load_mgh at 158
switch type
Error in ==> MRIread at 88
[mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in ==> make_outer_surface at 24
vol=MRIread(filled_volume);
>>
ERROR: make_outer_surface did not create output file
'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Linux localhost.localdomain 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007
i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue Jan 20 14:43:55 CET 2009
[r...@localhost christian]$
--
Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen:
http://www.gmx.net/de/go/multimessenger
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
