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CBICA / CaPTk

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
https://www.cbica.upenn.edu/captk
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Netlib routine lbfgs failed, Brain Mask was not written #1487

Closed camarasu closed 2 years ago

camarasu commented 2 years ago

Describe the bug When making command-line calls to the BraTSPipeline executable I get this error message, which prevents the brain mask completion:

mvnl_lbfgs: Error. Netlib routine lbfgs failed.
vnl_lbfgs: Error. Netlib routine lbfgs failed.
vnl_lbfgs: Error. Netlib routine lbfgs failed.
The version of model is incompatible with this version of CaPTk.
Brain Mask was not written, cannot proceed.

Please note that the first part of the pipeline executes correctly:

Executing with the default number of threads: 8
Number of NaNs: fixed: 0, moving 0
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -11076.5 GNORM= 33.9712
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 2 -11106.069 30.352 0.029
[...]

Generating image for T2 registered to the atlas.
Greedy command: /work/CaPTk/bin/install/appdir/usr/bin/greedy -d 3 -a -m NMI -i sorina/T1CE_rai_n4.nii.gz sorina/T2_rai_n4.nii.gz -o sorina/T2_to_T1CE.mat -ia-image-centers -n 100x50x10 -dof 6
Starting skull-stripping using DeepMedic.
Command for DeepMedic: /work/CaPTk/bin/install/appdir/usr/bin/DeepMedic -md /work/CaPTk/bin/install/appdir/usr/bin/../data//deepMedic/saved_models/skullStripping/ -i sorina/T1_to_SRI.nii.gz,sorina/T1CE_to_SRI.nii.gz,sorina/T2_to_SRI.nii.gz,sorina/FL_to_SRI.nii.gz -o sorina/dmOut_skull/brainMask_SRI.nii.gz

To Reproduce Build a Docker image using the Dockerfile (without its last line, concerning the GUI) and the current version of the software available in github.
Command line example :

/work/CaPTk/bin/install/appdir/usr/bin/BraTSPipeline -t1c CDIN_AXI_T1_3D_GADO.nii.gz -t1 CDIN_SAG_T1_FFE.nii.gz -t2 CDIN_AXI_T2_3_5_mm.nii.gz -fl CDIN_AXI_FLAIR.nii.gz -o sorina

CaPTk Version 1.9.0.Alpha

Desktop (please complete the following information):

AlexanderGetka-cbica commented 2 years ago

Hi @camarasu, thanks for your interest in CaPTk. I'm looking into this. Normally, the netlib routine failure messages don't actually cause the process to fail ( for example, I see these when registering sometimes with the desktop version of the app, but it doesn't halt).

The 1.9.0.Alpha had an issue wherein DeepMedic based models failed to run -- that also applied to skull stripping. So I think the error is occurring there.

Since the 1.9.0.RC build is now committed to master, the repo Dockerfile should now pull those changes based on the latest commits and should fix this issue. Can you please try that by re-building? You may need to pass --no-cache or similar to docker build to get it to rebuild with the latest code.

If that doesn't work, please let me know and I'll investigate further.

camarasu commented 2 years ago

Thank you very much @AlexanderGetka-cbica for your reply and suggested solution! I confirm that the 1.9.0.RC build fixes the issue.

AlexanderGetka-cbica commented 2 years ago

Great!

Closing this issue. Feel free to open a new issue if any other difficulties arise.