Hi Marie:

I am trying to run the LGI algorithm on 32 brains. As shown in the archives, I set the environment (on tcsh) and provided the MATLAB pathway.

[afrancis-mac:~] afrancis% setenv MATLABPATH /Applications/MATLAB_R2015a.app/ [afrancis-mac:~] afrancis% setenv PATH ${MATLABPATH}/bin:${PATH}

I also do have the Image processing toolbox. I got the following error:

Current: /Applications/freesurfer Previous: /cm/shared/freesurfer /Applications/freesurfer/subjects/DM99/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Aug 31 13:37:51 EDT 2016 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Applications/freesurfer/subjects/DM99/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('/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit =================

< M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015a (8.5.0.197613) 64-bit (maci64) February 12, 2015

For online documentation, see http://www.mathworks.com/support For product information, visit www.mathworks.com.

Academic License

...

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 '/Applications/freesurfer/subjects/DM99/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64

recon-all -s DM99 exited with ERRORS at Wed Aug 31 13:38:36 EDT 2016

For more details, see the log file /Applications/freesurfer/subjects/DM99/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

thanks so much,

best regards,

Alan