matlab is crashed when I run the pipeline

[Liang-He-Harlan]

I have encountered some issues when applying your pipeline to my research. I started with the signed_distance_isosurface function to validate whether I have successfully installed gptoolbox .

Issues:

I try to run the code on Matlab 2018b to check installment of pipeline:

Pial = gifti(pialSurfLHFile);
C = Pial.faces;
D = Pial.vertices;

[V,F] = signed_distance_isosurface(D,C,'Level',10,'GridSize',400);

Here, the structure of the Pial surface and variables are shown below.

Then my matlab was crashed: the crash report is below .txt file: matlab_crash_dump.txt

Here are some steps and the results to install the pipeline:

cd external/toolbox_fast_marching/
compile_mex

Also, I tried to cmake and make in the mex folder

mkdir build
cd build
cmake ..    # and also try `cmake .. -DMatlab_ROOT_DIR=/usr/local/MATLAB/R2018b/ -DCMAKE_TOOLCHAIN_FILE=/home/liang/vcpkg/scripts/buildsystems/vcpkg.cmake`
make

I also tried to replace the libstdc++.so.6

cd /usr/local/MATLAB/R2018b/sys/os/glnxa64/
sudo mv libstdc++.so.6 libstdc++.so.6.backup

sudo ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/local/MATLAB/R2018b/sys/os/glnxa64/libstdc++.so.6

However, the issue still exists.

[alecjacobson]

Could you please share what you ran from Matlab and any data needed to reproduce?

On Wed, Oct 9, 2024, 11:23 AM liang he @.***> wrote:

I have encountered some issues when applying your pipeline to my research. I started with the signed_distance_isosurface function to validate whether I have successfully installed gptoolbox .

Issues:

I try to run the code on Matlab 2018b to check installment of pipeline:

Pial = gifti(pialSurfLHFile); C = Pial.faces; D = Pial.vertices;

[V,F] = signed_distance_isosurface(D,C,'Level',10,'GridSize',400);

Here, the structure of the Pial surface and variables are shown below. f1.png (view on web) https://github.com/user-attachments/assets/88a36d1d-1e4a-4c77-a684-5e1711f14774 f2.png (view on web) https://github.com/user-attachments/assets/48437daa-6a0e-4ecd-8977-242eb34bb6b7

Then my matlab was crashed: the crash report is below .txt file: matlab_crash_dump.txt https://github.com/user-attachments/files/17310692/matlab_crash_dump.txt

Here are some steps and the results to install the pipeline:

cd external/toolbox_fast_marching/compile_mex

f3.png (view on web) https://github.com/user-attachments/assets/aa13b9bc-e56a-4310-9f42-a84117295982

Also, I tried to cmake and make in the mex folder

mkdir buildcd build cmake ..    # and also try cmake .. -DMatlab_ROOT_DIR=/usr/local/MATLAB/R2018b/ -DCMAKE_TOOLCHAIN_FILE=/home/liang/vcpkg/scripts/buildsystems/vcpkg.cmake make

f4.png (view on web) https://github.com/user-attachments/assets/1a62054e-d803-4292-ab91-3736b84560b9 f5.png (view on web) https://github.com/user-attachments/assets/5cd0d748-b9f6-4942-8396-239a1d40922b

I also tried to replace the libstdc++.so.6

cd /usr/local/MATLAB/R2018b/sys/os/glnxa64/ sudo mv libstdc++.so.6 libstdc++.so.6.backup

sudo ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/local/MATLAB/R2018b/sys/os/glnxa64/libstdc++.so.6

However, the issue still exists.

— Reply to this email directly, view it on GitHub https://github.com/alecjacobson/gptoolbox/issues/166, or unsubscribe https://github.com/notifications/unsubscribe-auth/AARDJGKGO3DYMEUSFJEDBHDZ2VDAPAVCNFSM6AAAAABPUZSC4KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU3TMMRVGE2TGOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[Liang-He-Harlan]

Dear alecjacobson,

Attachments are .m code and .mat file. Thank you for your help!

Best, Liang

---

发件人: Alec Jacobson @.> 发送时间: 2024年10月9日 11:42 收件人: alecjacobson/gptoolbox @.> 抄送: liang he @.>; Author @.> 主题: Re: [alecjacobson/gptoolbox] matlab is crashed when I run the pipeline (Issue #166)

Could you please share what you ran from Matlab and any data needed to reproduce?

On Wed, Oct 9, 2024, 11:23 AM liang he @.***> wrote:

I have encountered some issues when applying your pipeline to my research. I started with the signed_distance_isosurface function to validate whether I have successfully installed gptoolbox .

Issues:

I try to run the code on Matlab 2018b to check installment of pipeline:

Pial = gifti(pialSurfLHFile); C = Pial.faces; D = Pial.vertices;

[V,F] = signed_distance_isosurface(D,C,'Level',10,'GridSize',400);

Here, the structure of the Pial surface and variables are shown below. f1.png (view on web) https://github.com/user-attachments/assets/88a36d1d-1e4a-4c77-a684-5e1711f14774 f2.png (view on web) https://github.com/user-attachments/assets/48437daa-6a0e-4ecd-8977-242eb34bb6b7

Then my matlab was crashed: the crash report is below .txt file: matlab_crash_dump.txt https://github.com/user-attachments/files/17310692/matlab_crash_dump.txt

Here are some steps and the results to install the pipeline:

cd external/toolbox_fast_marching/compile_mex

f3.png (view on web) https://github.com/user-attachments/assets/aa13b9bc-e56a-4310-9f42-a84117295982

Also, I tried to cmake and make in the mex folder

mkdir buildcd build cmake ..    # and also try cmake .. -DMatlab_ROOT_DIR=/usr/local/MATLAB/R2018b/ -DCMAKE_TOOLCHAIN_FILE=/home/liang/vcpkg/scripts/buildsystems/vcpkg.cmake make

f4.png (view on web) https://github.com/user-attachments/assets/1a62054e-d803-4292-ab91-3736b84560b9 f5.png (view on web) https://github.com/user-attachments/assets/5cd0d748-b9f6-4942-8396-239a1d40922b

I also tried to replace the libstdc++.so.6

cd /usr/local/MATLAB/R2018b/sys/os/glnxa64/ sudo mv libstdc++.so.6 libstdc++.so.6.backup

sudo ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/local/MATLAB/R2018b/sys/os/glnxa64/libstdc++.so.6

However, the issue still exists.

— Reply to this email directly, view it on GitHub https://github.com/alecjacobson/gptoolbox/issues/166, or unsubscribe https://github.com/notifications/unsubscribe-auth/AARDJGKGO3DYMEUSFJEDBHDZ2VDAPAVCNFSM6AAAAABPUZSC4KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU3TMMRVGE2TGOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/alecjacobson/gptoolbox/issues/166#issuecomment-2402687873, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BC4HGAUYCWQ7RKSW2NBADGTZ2VFEVAVCNFSM6AAAAABPUZSC4KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBSGY4DOOBXGM. You are receiving this because you authored the thread.Message ID: @.***>

gptool = '/home/liang/Malab_Code/Packages/gptoolbox/';

addpath(strjoin(strcat([gptool],{'external','imageprocessing', 'images', 'matrix', 'mesh', 'mex', 'quat','utility','wrappers'}),':'))

% This is original code of loading surface % pialSurfLHFile = 'L.pial_MSMAll.32k_fs_LR.surf.gii'; % % Pial = gifti(pialSurfLHFile); % C = Pial.faces; % D = Pial.vertices;

% to load using .mat load('L_pial_MSMAll.mat');

C = pial.faces; D = pial.vertices;

[V,F] = signed_distance_isosurface(D,C,'Level',10,'GridSize',400);