Convert between MultiVolume and Volume Sequence?

Support
21

I would suggest two possible approaches, one using multivolumes, and one staying with sequences.

  • If you want to continue to use multivolume explorer, try steps 1-5 of the reply above (Convert between MultiVolume and Volume Sequence? - #4 by mikebind). This worked for me to successfully convert a registered volume sequence back to a multivolume.
  • If you are open to a different approach which will not rely on the outdated multivolume infrastructure, I would suggest segmenting your region of interest in Segment Editor with the first volume of the sequence as the master volume (setting the segmentation geometry). Then, use the Segment Statistics module to find the average voxel value in your segment. If you step through the frames of your sequence, you can gather the average voxel value in the segment for each frame. Once you have verified that you can successfully carry out this process, you can automate it with a python scripted module fairly easily.
22

Hi,
Sorry to bump an old thread, but I think the context here might be useful.

Iā€™m trying to use PkModelling with Volume Sequences. I run into an error:

vtkMRMLSequenceStorageNode::WriteDataInternal: No file extension recognized: /private/var/folders/_3/5s_kvnhj53x7sny2_71tf3lr0000gp/T/Slicer-gil2a4/BIJDD_vtkMRMLSequenceNodeBA.nrrd


ERROR writing file /private/var/folders/_3/5s_kvnhj53x7sny2_71tf3lr0000gp/T/Slicer-gil2a4/BIJDD_vtkMRMLSequenceNodeBA.nrrd

Happy to help further debug, but not sure how.

As far as I can tell, PkModelling (maybe all Slicer extensions?) saves out the inputs to temp files and runs a command line job on them. It tries to save them out to an .nrrd file (not sure where this is defined or if it can be changed). But the Sequence class seems only to be able to write to .mrb: https://github.com/Slicer/Slicer/blob/main/Libs/MRML/Core/vtkMRMLSequenceStorageNode.cxx#L148-L203

Should the sequence node be able to write as a dynamic .nrrd file?