Editing DTI brain mask on Mac

Support
#1

Operating system: Mac
Slicer version: 4.10.2
Expected behavior: Has editor module
Actual behavior: No editor module

Hi everyone
I normally run my DTI analysis using Windows, but wanted to try out whitematteranalysis and moved to a Mac to test it out. Normally on Windows (running 4.10.1) when I run “Diffusion Brain Masking” I am able to edit the mask to include extra areas (optic nerves). However, this module is not available on 4.10.2. Moving forward, I’m wondering if there’s another way I can edit the brain mask generated without downgrading to 4.10.1?

Thanks,
AC

#2

Maybe this is the same question as this issue:

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#3

Thanks Steve
I’m not sure how I missed it before…

However, I know the Editor module is being replaced by Segment Editor. I tried editing the mask using the Segment Editor but there’s no option to do so. Is it possible?

#4

@LearningSlicerYay - at the bottom of the Segmentations module there’s an import/export option that lets you bring in labelmaps as segmentations. Then you can export them again if you need a labelmap for other processing.

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#5

To convert with 2 mouse clicks, you can also go to Data module and right-click on the labelmap or segmentation node and choose to convert to segmentation or labelmap.

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#6

Hi all,

I’ve tried running this a couple times but every time I edit the brainmask and then try to run the DTI estimation, I get the following error:

Diffusion Tensor Estimation standard error:
C:/…/NA-MIC/Extensions-27931/SlicerDMRI/lib/Slicer-4.10/cli-modules/DWIToDTIEstimation.exe: Error reading Mask file, wrong coordinate space

This occurs regardless if I use the segmentations module to convert/edit/export the mask, or use the data module to convert/edit/export the mask. I’ve also tried editing the mask using the baseline and dwi as my master volumes but still get this error.

I am not sure how to overcome this one… Does anyone have any ideas?
(However, using the Editor module to edit the brainmask does not seem to result in this error).

#7

You can check the tensor estimation code is checking the transforms. You can look at this in the Volume Information tab of the Volumes module. The exported labelmap should match the master volume used to generate the segmentation.

#8

Hi Steve,

Thanks for your response. I’m not sure how to check whether the code is checking the transforms due to my limited coding/programming knowledge…

However, I think you’re on the right track as my dwi, baseline, and brainmask have the same spacing and origin (with some floating number differences), whereas the ones I converted have very different origins. I tried centering my dwi and the converted/exported brain masks but the origin is still different from my DWI. Manually changing the origin of the masks to the dwi / baseline still gives me the error above, and visually in the viewer shifts the mask significantly AWAY from the brain from my dwi/baseline.

EDIT: I actually noticed an extra menu on the export portion of the segmentation module where I can specify the master volume. Ensuring this is the DWI seems to have fixed the problem! : )

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