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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