Hi Marie:
I am trying to run the LGI post processing step on 60 ASD subjects. I am
using FreeSurfer 5.3. The recons went well and the processed brains look
great. However when I run the LGI step, I am getting the following error
which is as follows: Could you please help me?
[alanf@micc FreeSurfer_5.3]$ recon-all -s Asperger1 -localGI
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3
Actual FREESURFER_HOME /cm/shared/freesurfer
-rwxr-xr-x 1 alanf fiarl 963340 Apr 30 10:30
/data/alanf/FreeSurfer_5.3/Asperger1/scripts/recon-all.log
Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64
x86_64 x86_64 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /cm/shared/freesurfer
Previous: /usr/local/freesurfer/stable5_3_0/
/data/alanf/FreeSurfer_5.3/Asperger1/surf
#--------------------------------------------
#@# Local Gyrification Index lh Thu Apr 30 10:35:41 EDT 2015
mris_compute_lgi --i lh.pial
=================
rm -Rf
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to
/data/alanf/FreeSurfer_5.3/Asperger1/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('/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=================
< M A T L A B (R) >
Copyright 1984-2014 The MathWorks, Inc.
R2014a (8.3.0.532) 64-bit (glnxa64)
February 11, 2014
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> reading filled volume...
closing volume...
Undefined function 'fspecial' for input arguments of type 'char'.
Error in make_outer_surface (line 31)
Gaussian = fspecial('gaussian',[2 2],1);
>>
ERROR: make_outer_surface did not create output file
'/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64
x86_64 x86_64 GNU/Linux
recon-all -s Asperger1 exited with ERRORS at Thu Apr 30 10:35:55 EDT 2015
--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
*Alan N. Francis PhD*
NIDA T32 Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu <ezra_wegbr...@brown.edu>
afran...@mclean.harvard.edu
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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