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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