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Hello, Vittal,
do you have image processing toolbox of MATLAB installed? The function fspecial is part of this toolbox.
Antonin
Hello FS experts,I am trying to run the gyrification index and not able to move in the right direction. When execute this command "recon-all -s CSRI005 -localGI" and here is the output copied from the terminal "#@# Local Gyrification Index lh Wed Jul 10 13:15:03 IST 2019
mris_compute_lgi --i lh.pial
================= rm -Rf /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= rm: cannot remove '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz': Permission denied ================= mkdir -p /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... mghWrite(/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz, -1): could not open file conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit =================
Academic License
reading filled volume...
closing volume... Undefined function or variable 'fspecial'.
Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1);
ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux naren123 4.15.0-54-generic #58~16.04.1-Ubuntu SMP Mon Jun 24 13:21:41 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s CSRI005 exited with ERRORS at Wed Jul 10 13:15:10 IST 2019"
Also I have set the MATLAB path for freesurfer and here is the startup.m file
"%------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) addpath(genpath(fsmatlab)); end clear fshome fsmatlab; %-----------------------------------------------------%
%------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% "
I guess the error is because of 2 different user name: I have matlab license in X name and FreeSurfer can only be executed with root i.e. say Y. I mentioned both the information above. Wanna know the way to sort out this issue asap.
Waiting for your reply.
Thanks & regards Vittal