External Email - Use Caution
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
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>
>
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