External Email - Use Caution
Dear Douglas,
So to accomplish this, should I do the following through matlab?
The following code has to be in matlab’s startup.m file:
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%------------ FreeSurfer -----------------------------%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
%-----------------------------------------------------%
Also, if you are getting “ERROR: Matlab is required to run
mris_compute_lgi!”, it means your have to add the Matlab path to
Freesurfer`s $PATH variable for it to run.
To do this automatically when starting FS, just edit the .tcshrc file
(assuming you run FS from TCSH) adding the location of your Matlab’s bin
folder:
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setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
Thanks,
Alex
On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:
> You need to have matlab in your path so that when you type "matlab" it
> starts matlab
>
> On 7/9/2020 4:58 PM, Lab of Autism and Developmental Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I'm needing some simple help running LGI. After downloading MATLAB + Image
> processing toolbox and double checking if the ?h.pial file is located in
> the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still
> doesn't work. The output says that I still didn't install matlab onto my
> computer, so maybe it has something to do with setting
> $FREESURFER_HOME/matlab in your matlab path setup in your ~/matlab/starup.m
> script, but I'm unsure how to do this. Please see the output below:
>
> Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI
> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> INFO: SUBJECTS_DIR is /Applications/ace_complete
> Actual FREESURFER_HOME /Applications/freesurfer
> -rw-rw-r-- 1 ajobsaid 982768932 959822 Jul 9 10:50
> /Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log
> Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20
> 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
> /Applications/ace_complete/HAR30003_srs2_2/mri/transforms
> /Applications/ace_complete/HAR30003_srs2_2
> /Applications/ace_complete/HAR30003_srs2_2
> #@# white curv lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
> Update not needed
> #@# white area lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
> Update not needed
> #@# pial curv lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
> Update not needed
> #@# pial area lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
> Update not needed
> #@# thickness lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
> Update not needed
> #@# area and vertex vol lh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> ../surf/lh.thickness
> Update not needed
> #@# white curv rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
> Update not needed
> #@# white area rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
> Update not needed
> #@# pial curv rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
> Update not needed
> #@# pial area rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
> Update not needed
> #@# thickness rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
> Update not needed
> #@# area and vertex vol rh Thu Jul 9 12:58:04 PDT 2020
> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> ../surf/rh.thickness
> Update not needed
> /Applications/ace_complete/HAR30003_srs2_2/surf
> #--------------------------------------------
> #@# Local Gyrification Index lh Thu Jul 9 12:58:04 PDT 2020
> \n mris_compute_lgi --i lh.pial \n
> ERROR: Matlab is required to run mris_compute_lgi!
> Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20
> 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
>
> recon-all -s HAR30003_srs2_2 exited with ERRORS at Thu Jul 9 12:58:04 PDT
> 2020
>
> Thanks,
> Alex
>
>
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