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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