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

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:

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%------------ 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


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