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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