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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: 1 2 3 4 5 6 7 8 9 %------------ 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 $PATH variable for it to run.
To do this automatically when starting FS, just edit the .tcshrc file (assuming you run FS from TCSH) adding the location of your Matlab’s bin folder: 1 setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
Thanks, Alex
On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve dgreve@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 CautionDear 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Freesurfer experts,
I have added Matlab my path and either the same error (please see my first email) occurs, or recon-all -s (ID) -localGI command is said to 'not exist'. Any other ideas on how to properly solve this problem? Thank you and hope everyone is safe!
On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> wrote:
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: 1 2 3 4 5 6 7 8 9 %------------ 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 $PATH variable for it to run.
To do this automatically when starting FS, just edit the .tcshrc file (assuming you run FS from TCSH) adding the location of your Matlab’s bin folder: 1 setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
Thanks, Alex
On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve dgreve@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 CautionDear 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If you type matlab at the command line, does matlab start?
On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:
External Email - Use Caution
Dear Freesurfer experts,
I have added Matlab my path and either the same error (please see my first email) occurs, or recon-all -s (ID) -localGI command is said to 'not exist'. Any other ideas on how to properly solve this problem? Thank you and hope everyone is safe!
On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn@email.gwu.edu mailto:ladn@email.gwu.edu> wrote:
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: 1 2 3 4 5 6 7 8 9 %------------FreeSurfer-----------------------------% fshome=getenv('FREESURFER_HOME'); fsmatlab=sprintf('%s/matlab',fshome); if(exist(fsmatlab)==7) path(path,fsmatlab); end clearfshome 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 $PATH variable for it to run. To do this automatically when starting FS, just edit the .tcshrc file (assuming you run FS from TCSH) adding the location of your Matlab’s bin folder: 1 setenv PATH"/Applications/MATLAB_R2014a.app/bin":"$PATH" Thanks, Alex On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Douglas,
Yes, now matlab is correctly set to my freesurfer path, but the following error occurs when I run localGI (please see below). Any ideas what might be wrong? Maybe there are some issues with the matlab version or image processing toolbox that I'm using?
iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 -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/BAP_complete Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 ajobsaid 982768932 956144 Jun 30 09:20 /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64 /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms /Applications/BAP_complete/nih00024_epoch11_4 /Applications/BAP_complete/nih00024_epoch11_4 #@# white curv lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /Applications/BAP_complete/nih00024_epoch11_4/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit =================
< M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020a Update 3 (9.8.0.1396136) 64-bit (maci64) May 27, 2020
Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a/bin Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020 Warning: Name is nonexistent or not a directory: /private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
reading filled volume...
closing volume... morphological closing done. writing outer surface...
================= mris_extract_main_component /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main =================
counting number of connected components... 72876 voxel in cpt #1: X=2 [v=72876,e=218622,f=145748] located at (-25.312176, -9.845789, 0.428207) For the whole surface: X=2 [v=72876,e=218622,f=145748] One single component has been found nothing to do done
================= mris_smooth -nw -n 30 /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 72876 - 218622 + 145748 = 2 --> 0 holes F =2V-4: 145748 = 145752-4 (0) 2E=3F: 437244 = 437244 (0)
total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_37963_.m'); exit =================
< M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020a Update 3 (9.8.0.1396136) 64-bit (maci64) May 27, 2020
Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a/bin Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020 Warning: Name is nonexistent or not a directory: /private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
Warning: Argument must be a string scalar or character vector.
In ver (line 45)
In freesurfer_read_surf (line 70) In find_corresponding_center_FSformat (line 26) Error using fprintf Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
ERROR: find_corresponding_center_FSformat did not complete successfully! Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
recon-all -s nih00024_epoch11_4 exited with ERRORS at Fri Jul 31 09:20:20 PDT 2020
For more details, see the log file /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Jul 15, 2020 at 9:46 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
If you type matlab at the command line, does matlab start?
On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:
External Email - Use CautionDear Freesurfer experts,
I have added Matlab my path and either the same error (please see my first email) occurs, or recon-all -s (ID) -localGI command is said to 'not exist'. Any other ideas on how to properly solve this problem? Thank you and hope everyone is safe!
On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> wrote:
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: 1 2 3 4 5 6 7 8 9 %------------ 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 $PATH variable for it to run.
To do this automatically when starting FS, just edit the .tcshrc file (assuming you run FS from TCSH) adding the location of your Matlab’s bin folder: 1 setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
Thanks, Alex
On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve dgreve@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 CautionDear 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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Dear Freesurfer experts,
Just wanted to follow up my last email - does anyone know what might be wrong with my code?
Thank you and stay safe, Alex
On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> wrote:
Dear Douglas,
Yes, now matlab is correctly set to my freesurfer path, but the following error occurs when I run localGI (please see below). Any ideas what might be wrong? Maybe there are some issues with the matlab version or image processing toolbox that I'm using?
iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 -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/BAP_complete Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 ajobsaid 982768932 956144 Jun 30 09:20 /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64 /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms /Applications/BAP_complete/nih00024_epoch11_4 /Applications/BAP_complete/nih00024_epoch11_4 #@# white curv lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /Applications/BAP_complete/nih00024_epoch11_4/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit =================
< M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020a Update 3 (9.8.0.1396136) 64-bit (maci64) May 27, 2020Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a/bin Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020 Warning: Name is nonexistent or not a directory: /private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
reading filled volume...
closing volume... morphological closing done. writing outer surface...
================= mris_extract_main_component /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main =================
counting number of connected components... 72876 voxel in cpt #1: X=2 [v=72876,e=218622,f=145748] located at (-25.312176, -9.845789, 0.428207) For the whole surface: X=2 [v=72876,e=218622,f=145748] One single component has been found nothing to do done
================= mris_smooth -nw -n 30 /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 72876 - 218622 + 145748 = 2 --> 0 holes F =2V-4: 145748 = 145752-4 (0) 2E=3F: 437244 = 437244 (0)
total defect index = 0
mris_convert -n lh.pial-outer-smoothed /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_37963_.m'); exit =================
< M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020a Update 3 (9.8.0.1396136) 64-bit (maci64) May 27, 2020Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a/bin Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020 Warning: Name is nonexistent or not a directory: /private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
Warning: Argument must be a string scalar or character vector.
In ver (line 45)
In freesurfer_read_surf (line 70) In find_corresponding_center_FSformat (line 26) Error using fprintf Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
ERROR: find_corresponding_center_FSformat did not complete successfully! Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
recon-all -s nih00024_epoch11_4 exited with ERRORS at Fri Jul 31 09:20:20 PDT 2020
For more details, see the log file /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Jul 15, 2020 at 9:46 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
If you type matlab at the command line, does matlab start?
On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:
External Email - Use CautionDear Freesurfer experts,
I have added Matlab my path and either the same error (please see my first email) occurs, or recon-all -s (ID) -localGI command is said to 'not exist'. Any other ideas on how to properly solve this problem? Thank you and hope everyone is safe!
On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> wrote:
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: 1 2 3 4 5 6 7 8 9 %------------ 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 $PATH variable for it to run.
To do this automatically when starting FS, just edit the .tcshrc file (assuming you run FS from TCSH) adding the location of your Matlab’s bin folder: 1 setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
Thanks, Alex
On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve < dgreve@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 CautionDear 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Looks like something is wrong with the Matlab installation. It would be good to know:
1) What happens if you type 'matlab' in your shell? 2) What happens if you type '/Applications/MATLAB_R2020a/bin/matlab' in your shell?
Best,
Tim
On August 4, 2020 at 8:31 PM "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" ladn@email.gwu.edu wrote:
External Email - Use CautionDear Freesurfer experts,
Just wanted to follow up my last email - does anyone know what might be wrong with my code?
Thank you and stay safe, Alex
On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> wrote:
Dear Douglas,
Yes, now matlab is correctly set to my freesurfer path, but the following error occurs when I run localGI (please see below). Any ideas what might be wrong? Maybe there are some issues with the matlab version or image processing toolbox that I'm using?
iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4 -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/BAP_complete Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 ajobsaid 982768932 956144 Jun 30 09:20 /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64 /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms /Applications/BAP_complete/nih00024_epoch11_4 /Applications/BAP_complete/nih00024_epoch11_4 #@# white curv lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /Applications/BAP_complete/nih00024_epoch11_4/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit =================
< M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020a Update 3 (9.8.0.1396136) 64-bit (maci64) May 27, 2020Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a/bin Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020 Warning: Name is nonexistent or not a directory: /private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
reading filled volume...
closing volume... morphological closing done. writing outer surface...
================= mris_extract_main_component /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main =================
counting number of connected components... 72876 voxel in cpt #1: X=2 [v=72876,e=218622,f=145748] located at (-25.312176, -9.845789, 0.428207) For the whole surface: X=2 [v=72876,e=218622,f=145748] One single component has been found nothing to do done
================= mris_smooth -nw -n 30 /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 72876 - 218622 + 145748 = 2 --> 0 holes F =2V-4: 145748 = 145752-4 (0) 2E=3F: 437244 = 437244 (0)
total defect index = 0
mris_convert -n lh.pial-outer-smoothed /Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_37963_.m'); exit =================
< M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020a Update 3 (9.8.0.1396136) 64-bit (maci64) May 27, 2020Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a/bin Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020 Warning: Name is nonexistent or not a directory: /private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
Warning: Argument must be a string scalar or character vector.
In ver (line 45)
In freesurfer_read_surf (line 70) In find_corresponding_center_FSformat (line 26) Error using fprintf Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
ERROR: find_corresponding_center_FSformat did not complete successfully! Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
recon-all -s nih00024_epoch11_4 exited with ERRORS at Fri Jul 31 09:20:20 PDT 2020
For more details, see the log file /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Jul 15, 2020 at 9:46 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
If you type matlab at the command line, does matlab start?
On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:
External Email - Use CautionDear Freesurfer experts,
I have added Matlab my path and either the same error (please see my first email) occurs, or recon-all -s (ID) -localGI command is said to 'not exist'. Any other ideas on how to properly solve this problem? Thank you and hope everyone is safe!
On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> wrote:
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: 1 2 3 4 5 6 7 8 9 %------------ 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 $PATH variable for it to run.
To do this automatically when starting FS, just edit the .tcshrc file (assuming you run FS from TCSH) adding the location of your Matlab’s bin folder: 1 setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
Thanks, Alex
On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve < dgreve@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 CautionDear 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
Dear Tim,
1) Here is the output after I type matlab: - Matlab does open, and the following appears on terminal: shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory pwd: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory pwd: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory GVA encoder info: AMD performance mode : 2 GVA encoder info: deleteSCDMetalContext : texture cache hits: 0, misses: 0
2) and /Applications/MATLAB_R2020a/bin/matlab: /Applications/MATLAB_R2020a/bin/matlab: No such file or directory
Please let me know if you need more information.
Thank you, Alex
On Wed, Aug 5, 2020 at 3:42 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionLooks like something is wrong with the Matlab installation. It would be good to know:
- What happens if you type 'matlab' in your shell?
- What happens if you type '/Applications/MATLAB_R2020a/bin/matlab' in
your shell?
Best,
Tim
On August 4, 2020 at 8:31 PM "Lab of Autism and Developmental
Neuroscience, Lab of Autism and Developmental Neuroscience" < ladn@email.gwu.edu> wrote:
External Email - Use CautionDear Freesurfer experts,
Just wanted to follow up my last email - does anyone know what might be wrong with my code?
Thank you and stay safe, Alex
On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> wrote:
Dear Douglas,
Yes, now matlab is correctly set to my freesurfer path, but the
following
error occurs when I run localGI (please see below). Any ideas what
might be
wrong? Maybe there are some issues with the matlab version or image processing toolbox that I'm using?
iMac-Pro:BAP_complete ajobsaid$ recon-all -s nih00024_epoch11_4
-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/BAP_complete Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 ajobsaid 982768932 956144 Jun 30 09:20 /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64 /Applications/BAP_complete/nih00024_epoch11_4/mri/transforms /Applications/BAP_complete/nih00024_epoch11_4 /Applications/BAP_complete/nih00024_epoch11_4 #@# white curv lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv Update not needed #@# white area lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area Update not needed #@# pial curv lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# thickness lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# area and vertex vol lh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness Update not needed #@# white curv rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv Update not needed #@# white area rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area Update not needed #@# pial curv rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed #@# thickness rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed #@# area and vertex vol rh Fri Jul 31 09:20:05 PDT 2020 cd /Applications/BAP_complete/nih00024_epoch11_4/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness Update not needed /Applications/BAP_complete/nih00024_epoch11_4/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Jul 31 09:20:05 PDT 2020 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
=================
mkdir -p
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial
=================
mris_fill -c -r 1 lh.pial
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
================= reading surface from lh.pial... writing filled volume to
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume setting resolution for intermediate calculations to 1.0000 =================
make_outer_surface('/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
< M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020a Update 3 (9.8.0.1396136) 64-bit (maci64) May 27, 2020Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a/bin Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a Warning: Name is nonexistent or not a directory:
/Applications/MATLAB_R2020
Warning: Name is nonexistent or not a directory: /private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
reading filled volume...
closing volume... morphological closing done. writing outer surface...
================= mris_extract_main_component
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
=================
counting number of connected components... 72876 voxel in cpt #1: X=2 [v=72876,e=218622,f=145748] located at (-25.312176, -9.845789, 0.428207) For the whole surface: X=2 [v=72876,e=218622,f=145748] One single component has been found nothing to do done
================= mris_smooth -nw -n 30
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
./lh.pial-outer-smoothed
smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 72876 - 218622 + 145748 = 2 --> 0 holes F =2V-4: 145748 = 145752-4 (0) 2E=3F: 437244 = 437244 (0)
total defect index = 0
mris_convert -n lh.pial-outer-smoothed
/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc
=================
find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/Applications/BAP_complete/nih00024_epoch11_4/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_37963_.m');
exit
< M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020a Update 3 (9.8.0.1396136) 64-bit (maci64) May 27, 2020Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a/bin Warning: Name is nonexistent or not a directory: /Applications/MATLAB_R2020a Warning: Name is nonexistent or not a directory:
/Applications/MATLAB_R2020
Warning: Name is nonexistent or not a directory: /private/var/folders/4z/2l_m9k0x5g1dxqfzjh5gws2mlw_d_j/T/Editor_vxdxq
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
Warning: Argument must be a string scalar or character vector.
In ver (line 45)
In freesurfer_read_surf (line 70) In find_corresponding_center_FSformat (line 26) Error using fprintf Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
ERROR: find_corresponding_center_FSformat did not complete
successfully!
Darwin iMac-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64 x86_64
recon-all -s nih00024_epoch11_4 exited with ERRORS at Fri Jul 31
09:20:20
PDT 2020
For more details, see the log file /Applications/BAP_complete/nih00024_epoch11_4/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Jul 15, 2020 at 9:46 AM Douglas N. Greve <
dgreve@mgh.harvard.edu>
wrote:
If you type matlab at the command line, does matlab start?
On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience,
Lab
of Autism and Developmental Neuroscience wrote:
External Email - Use CautionDear Freesurfer experts,
I have added Matlab my path and either the same error (please see my first email) occurs, or recon-all -s (ID) -localGI command is said to
'not
exist'. Any other ideas on how to properly solve this problem? Thank
you
and hope everyone is safe!
On Sat, Jul 11, 2020 at 11:48 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience < ladn@email.gwu.edu> wrote:
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: 1 2 3 4 5 6 7 8 9 %------------ 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 $PATH variable for it to run.
To do this automatically when starting FS, just edit the .tcshrc file (assuming you run FS from TCSH) adding the location of your Matlab’s
bin
folder: 1 setenv PATH "/Applications/MATLAB_R2014a.app/bin":"$PATH"
Thanks, Alex
On Fri, Jul 10, 2020 at 10:30 AM Douglas N. Greve < dgreve@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 CautionDear 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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-- Tim Schäfer
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freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience -
Tim Schäfer