Error computing Curved Multi-Planar Reformation (CMPR)

[carlos.alberto.bulant]

Hi all,

First of all, I would like to thank vmtk-developers for such a useful toolkit, I've been using it for several years now, and it is great! Allways from the command line, and recently from within python scripts.

I've trying to compute the Curved Multi-Planar Reformation (CMPR) of an image from a centerline, without success (from the command line nor my python script).

I get the folloing error when executing the vmtk.vtkvmtk.vtkvmtkCurvedMPRImageFilter (from my script) or vmtkimagecurvedmpr (from the terminal)

ERROR: In ../Common/DataModel/vtkImageData.cxx, line 1324

vtkImageData (0x202ede0): No Scalar Field has been specified - assuming 1 component!

I have been browsing the mailing list, and I found this thread. So I downloaded the data-sets and use the script indicated by Luca, but I get the same error.

I would appreciate any help.

Best regards,

Carlos

PS: I am running Ubuntu 20.04.1 LTS, with miniconda. My environment was created as follows:

conda install anaconda-client
conda update conda anaconda-client
conda config --set restore_free_channel true
conda create -n ccta-segmentation python=3.6
conda activate ccta-segmentation
conda install -c anaconda vtk=8.1.0
conda install -c vmtk vmtk  

conda install -c simpleitk simpleitk

conda install -c conda-forge scipy
conda install -c conda-forge scikit-learn

[carlos.alberto.bulant]

Hello everybody,

Thanks to, Camila García, that pointed me in the right direction!

I have been doing some digging on the subject and seems that there are other users struggling with vtkvmtkCurvedMPRImageFilter.

Some previous emails in the group are: 

https://groups.google.com/g/vmtk-users/c/pSI10B0_q1I/m/IXII35jrCgAJ

https://groups.google.com/g/vmtk-users/c/3ecjPLwis-A/m/Niyjaj8VCAAJ

https://groups.google.com/g/vmtk-users/c/FWUc9hbicq8/m/ICAbieZmAQAJ

https://groups.google.com/g/vmtk-users/c/CoGuS0FEDlU/m/92GkRmoQAAAJ

https://groups.google.com/g/vmtk-users/c/GZ7aZkeIglY/m/kHsY_m_xBQAJ

But the key here was this issue on the vmtk github.

As commented by Kohit, there is a missing scalars allocation for VTK_MAJOR_VERSION >7, near line 343 of the vtkVmtk/Misc/vtkvmtkCurvedMPRImageFilter.cxx file.

So adding the allocation on line 343 and re-compiling VMTK worked for me.

It would be nice if vmtk developers could made this fix available for the conda installation. But for now, I just created a new conda environment and compiled vmtk on it.

Best regards, and thank you again for the great work!

Carlos

[lu yee]

Hi.I have little experience about how to complie vmtk development version. Can you tell me how to  create a new conda environment and compiled vmtk on it ?

Thank you in advance.

[andra...@gmail.com]

Please post your question to the VMTK forum at

https://discourse.slicer.org/c/community/vmtk

 

Thank you,

Andras

--
You received this message because you are subscribed to the Google Groups "vmtk-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to vmtk-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/vmtk-users/de16f64b-446e-4c04-9639-cd2aa5c92df6n%40googlegroups.com.