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 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 Caution       
>
> 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, 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 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 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 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
> >>>
> >>>
> >> _______________________________________________
> >> 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
> >
> >
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Tim Schäfer

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