Hey there, I’m back with more silly questions using the examples of using segment editor have been really helpful, the issue I have been running into, however, is using an image that is not the sample image. Just dragging in an image and avoiding anything that uses ‘masterVolumeNode’ was my origi…

This example should work as is, just replace this line: masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1() by this, if you use recent 4.11 version of Slicer: masterVolumeNode = slicer.util.loadVolume('C:/Users/m222222/Dropbox/BRAIN_MASK.nii.gz') by this, if you use 4.10 version: [succes…

that makes a lot of sense, thank you

I replaced the first line with [success, masterVolumeNode] = slicer.util.loadVolume(“C:/Users/m214492/Dropbox/CNV Modeling/Brain for Gustavo/BRAIN_MASK.nii.gz”, returnNode=True) because it gave a syntax error the ran with one quote, and everything seemed to work until I got to that apply line eff…

I think it may have something to do with the fact that in the sample, slicer actually opens the file, and you can see it in your 3 colored windows, but when I set my master volume, the file doesn’t come up visibly in slicer. I’m not sure if that could be the issue or not.

Does the example that I linked above works? If yes then try to follow that example more closely, make modifications step-by-step, and see which change causes the problem.

The sample that is provided works without an issue, and slicer doesn’t throw up an error until the thresholding line (after going through the code step by step) effect.self().onApply() So there must be an issue earlier although there was no complaint from slicer. I believe that is has to do with l…

What is the output of print(master VolumeNode)?

It means the image loading has failed. The application log may contain more details (menu: Help / Report a bug). Is the file path correct? Can you load the image by using “Add data”?

When I use the ‘add data’ option I get [INFO][VTK] 02.08.2019 10:18:59 [vtkMRMLVolumeArchetypeStorageNode (0x7f9436777de0)] (/Volumes/Dashboards/Stable/Slicer-4102/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:465) - Loaded volume from file: /Users/m214492/Dropbox/CNV Modeling/Brain for Gust…

Segmentation using thresholding using Python

Development

Topic		Replies	Views
Automating segmentation on volumes Support	19	4172	December 30, 2019
Segmentation (Extract Skin Py) Development	5	952	October 5, 2019
Loading dicom directory into scene and obtaining master volume node Support segmentation , dicom	10	1225	March 26, 2020
Threshold scalar volume to labelmap Development volume , cli , filters	12	2254	June 4, 2021
Convert label map volume into a scalarvolumenode Support	20	3677	July 25, 2018

Segmentation using thresholding using Python

Related topics