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 <#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 <#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 GitHub<#166 (comment)>, or unsubscribe<https://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);

[alecjacobson]

Hi Liang,
I wonder if the attachments got lost in the email. Maybe try uploading them directly on the github conversation?

[Liang-He-Harlan]

Dear alecjacobson,

There are the code and data.
code_and_data.zip

As mentioned, the Matlab R2018b will crash in the Ubuntu 22.04 when I try to run the signed_distance_isosurface function from the gptoolbox.
Thank you for your support!

Best,
Liang

[alecjacobson]

Thanks! The issue is that your face list C is a int32 type.

All my functions pretty much assume that all data (including index lists; as is common in matlab) are double type.

So the easiest fix is:

C = double(C);
D = double(D); % maybe not necessary; but good idea for gptoolbox

It's possible for me to handle this better on the mex side instead, but not something I'm planning to fix.

[Liang-He-Harlan]

Dear alecjacobson,

It works now. Thanks for your support!

Best,
Liang