plumonary toolkit failure

[Arindam-1991]

I am getting the following error while segmenting lung field or lobel using the toolkit The plugin PTKlobes failed with the following error: Subscript indices must either be real positive integers or logicals.

[tomdoel]

Hi, which version are you using? There was an issue which was fixed in v1.0.1 which previoulsy caused this problem on some datasets. 1.0.1 is the latest version on git (not currently available as a pre-release).

[Rukhmini]

Currently,I am using v 1.0.0. How do I get the latest version? Also, the export segment saves the result only in axial view. How to export the segment in coronal and sagittal view?

[tomdoel]

Hi, I would recommend using git to clone the latest codebase https://github.com/tomdoel/pulmonarytoolkit.git and regularly updating with git pull (see git documentation for details, or use GitHub Desktop to do the same thing).

I would probably choose the MHD format when exporting segmentations, which will save out a 3D image. Then it is easy to load into other software if you want to reorder the dimensions. The default orientation of the image generally tries to match the original image orientation, so that input and segmentaiton image can be aligned. For Dicom, this allows each input and segmentaiton slice to be directly referenced to each other by DICOM viewers. It is possible to force a different export orientation by overridding the orientation variable in the save functions eg MimSaveImageAsDicom.m but that might cause problems with Dicom viewers since the Dicom model might no longer be correct.