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IDProjectCategoryView StatusLast Update
0004643Slicer4Module CropVolumepublic2018-10-26 10:57
ReporterNassirAAssigned Tofedorov 
Status acknowledgedResolutionopen 
Product VersionSlicer 4.8.1 
Target VersionFixed in Version 
Summary0004643: Expansion of CropVolume Spacing Scale Parameter to accomodate multiple scaling

I'm trying to resample an image only along the Zdirection using the module Crop Volume. The parameter Spacing Scale forces me to resample X and Y along with it, but this results in extremely large arrays. Could the parameter Spacing Scale be turned into a 3 option array?

TagsNo tags attached.




2018-10-18 13:51

developer   ~0016169

Last edited: 2018-10-18 13:51

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This makes a lot of sense to me, and should be easy to add, given the assumptions are right.

I am not actively contributing to the Slicer core application at the moment though, and a bit different priorities right now, so I am not sure when I will get to it (I don't even have the current Slicer trunk compiled).

@lassoan have been contributing features to this module lately, and it would probably be trivial for him to add this feature. He might also have strong opinions about the course of action, so I include him in the conversation. For example, I am not sure if Andras thinks of CropVolume as a tool that is supposed to handle arbitrary number of dimensions of input, or it is always expected to be 3d.



2018-10-18 14:50

developer   ~0016170

This "feature" is not just accidentally missing from the Crop volume module. Creating a non-isotropic volume essentially destroy volumetric data: you cannot really make use of the high-resolution within a slice if distance between slices is large. There could be valid reasons why you would want to do this anyway, but in general, users should not even consider doing this. Making this available in Crop volumes module properly would take a few days (add an advanced section where anisotropic spacing can be temporarily enabled, add new parameter to MRML node, make sure everything is backward compatible, etc.).

Instead, I would recommend to manually divide spacing value with a constant in the input volume manually, do isotropic resampling, and then multiply spacing value with the same constant. You may also use "Resample scalar volume" for resampling, which allows specifying different spacing values.



2018-10-25 18:34

reporter   ~0016176

Fair enough! The alternative gets me what I want. Thank you. If you're curious, I'm doing this to allow my low-Z-resolution Axial-volume-based-segmentation to use the information from my higher-Z-resolution Sagittal volume (otherwise, the segmentation Z size is limited to the axial geometry).

Sorry for the late response, and thanks again.



2018-10-25 19:27

developer   ~0016177

Binary labelmap the segmentation node can be of different resolution than the master volume. In recent Slicer versions there is a button on near the master volume selector that allows you to set an arbitrary resolution.



2018-10-25 19:30

developer   ~0016178

Also, it is strongly recommended to always make the segmentation have isotropic resolution (same spacing along all axes) even if you use only one anisotropic master volume.



2018-10-26 10:57

reporter   ~0016179

That's convenient! More thanks to you.

Issue History

Date Modified Username Field Change
2018-10-17 19:30 NassirA New Issue
2018-10-17 19:30 NassirA Status new => assigned
2018-10-17 19:30 NassirA Assigned To => fedorov
2018-10-18 13:44 NassirA Description Updated View Revisions
2018-10-18 13:45 NassirA Severity trivial => tweak
2018-10-18 13:51 fedorov Note Added: 0016169
2018-10-18 13:51 fedorov Note Edited: 0016169 View Revisions
2018-10-18 13:52 fedorov Status assigned => acknowledged
2018-10-18 14:50 lassoan Note Added: 0016170
2018-10-25 18:34 NassirA Note Added: 0016176
2018-10-25 19:27 lassoan Note Added: 0016177
2018-10-25 19:30 lassoan Note Added: 0016178
2018-10-26 10:57 NassirA Note Added: 0016179