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...@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" <
> l...@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 <
> > l...@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 <
> dgr...@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 <
> > >> l...@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 <
> > >>> dgr...@mgh.harvard.edu> wrote:
> > >>>
> > >>>> You need to have matlab in your path so that when you type "matlab"
> it
> > >>>> starts matlab
> > >>>>
> > >>>> On 7/9/2020 4:58 PM, Lab of Autism and Developmental Neuroscience,
> Lab
> > >>>> of Autism and Developmental Neuroscience wrote:
> > >>>>
> > >>>> External Email - Use Caution
> > >>>> Dear Freesurfer experts,
> > >>>>
> > >>>> I'm needing some simple help running LGI. After downloading MATLAB +
> > >>>> Image processing toolbox and double checking if the ?h.pial file is
> located
> > >>>> in the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command
> still
> > >>>> doesn't work. The output says that I still didn't install matlab
> onto my
> > >>>> computer, so maybe it has something to do with setting
> > >>>> $FREESURFER_HOME/matlab in your matlab path setup in your
> ~/matlab/starup.m
> > >>>> script, but I'm unsure how to do this. Please see the output below:
> > >>>>
> > >>>> Mac-Pro:ace_complete ajobsaid$ recon-all -s HAR30003_srs2_2 -localGI
> > >>>> Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> > >>>> Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
> > >>>> INFO: SUBJECTS_DIR is /Applications/ace_complete
> > >>>> Actual FREESURFER_HOME /Applications/freesurfer
> > >>>> -rw-rw-r-- 1 ajobsaid 982768932 959822 Jul 9 10:50
> > >>>> /Applications/ace_complete/HAR30003_srs2_2/scripts/recon-all.log
> > >>>> Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug
> 20
> > >>>> 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
> > >>>> /Applications/ace_complete/HAR30003_srs2_2/mri/transforms
> > >>>> /Applications/ace_complete/HAR30003_srs2_2
> > >>>> /Applications/ace_complete/HAR30003_srs2_2
> > >>>> #@# white curv lh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
> > >>>> Update not needed
> > >>>> #@# white area lh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
> > >>>> Update not needed
> > >>>> #@# pial curv lh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --curv-map ../surf/lh.pial 2 10
> ../surf/lh.curv.pial
> > >>>> Update not needed
> > >>>> #@# pial area lh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
> > >>>> Update not needed
> > >>>> #@# thickness lh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> > >>>> ../surf/lh.thickness
> > >>>> Update not needed
> > >>>> #@# area and vertex vol lh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5
> > >>>> ../surf/lh.thickness
> > >>>> Update not needed
> > >>>> #@# white curv rh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
> > >>>> Update not needed
> > >>>> #@# white area rh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
> > >>>> Update not needed
> > >>>> #@# pial curv rh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --curv-map ../surf/rh.pial 2 10
> ../surf/rh.curv.pial
> > >>>> Update not needed
> > >>>> #@# pial area rh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
> > >>>> Update not needed
> > >>>> #@# thickness rh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> > >>>> ../surf/rh.thickness
> > >>>> Update not needed
> > >>>> #@# area and vertex vol rh Thu Jul 9 12:58:04 PDT 2020
> > >>>> cd /Applications/ace_complete/HAR30003_srs2_2/mri
> > >>>> mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5
> > >>>> ../surf/rh.thickness
> > >>>> Update not needed
> > >>>> /Applications/ace_complete/HAR30003_srs2_2/surf
> > >>>> #--------------------------------------------
> > >>>> #@# Local Gyrification Index lh Thu Jul 9 12:58:04 PDT 2020
> > >>>> \n mris_compute_lgi --i lh.pial \n
> > >>>> ERROR: Matlab is required to run mris_compute_lgi!
> > >>>> Darwin iMac-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug
> 20
> > >>>> 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
> > >>>>
> > >>>> recon-all -s HAR30003_srs2_2 exited with ERRORS at Thu Jul 9
> 12:58:04
> > >>>> PDT 2020
> > >>>>
> > >>>> Thanks,
> > >>>> Alex
> > >>>>
> > >>>>
> > >>>> _______________________________________________
> > >>>> Freesurfer mailing listfreesur...@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 listfreesur...@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
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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