Hi Alan, Do you have the image processing toolbox installed in matlab? If not, I guess this is the source of the error.
Best, Marie On Apr 30, 2015, at 7:51 AM, Alan Francis <alandarkene...@gmail.com<mailto:alandarkene...@gmail.com>> wrote: 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<http://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<mailto:ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu<mailto:afran...@mclean.harvard.edu> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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