Limiting DTI computation to a masked region, axis re-oreintaton

To all,

  1. I am trying to limit the computation of the DTI data to a masked region (created using the segment editor) within the volume (in this case a human disc). For reference, I am trying to remove the green regions around the disc.
  2. How would re-Oriente the imaging planes ( green and yellow) windows to better match the disc anatomical axes

    Thank you, Ron

Andras hi, could ask for your help with the first issue? I hope to present next week, and it would be very helpful to be able to segment out all the data outside the disc segmentation. I think there used to be an option to use the segment label to restrict the region of DTI reconstruction. However, I cannot find a way to do so (only option is brain label?). Happy to share the slicer file. R

You can use “Mask volume” effect in Segment Editor to blank out voxels of a volume outside the current segment. Would that be sufficient for you?

You can use Crop volume module for this. You can enable rotation for the region of interest (by right-clicking on any of its control point and in check “Interaction options” → “Rotate”.

I hope so, I will try this now. Steve is also looking into this.

Trying to mask a DTI volume with the segment editor led to a crash (maybe not a surprise but still not good).

This method works after exporting the segmentation to a label:

>>> d = array("Output DTI*e")
>>> m = array("11-9001-pre_load-Segmentation-label")
>>> d[numpy.where(m != 1)] = numpy.zeros([3,3])

I’ll make new nrrd dti files for you Ron.


Steve Thanks!!!

Ron Noah Alkalay is inviting you to a scheduled Zoom meeting.

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Ron N Alkalay
Associate Professor,
Dept of Orthopedic Surgery, Harvard Medical School
Center for Advanced
Orthopedic Studies
Beth Israel
Deaconess Medical Center
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Thanks for your help with this @lassoan. I showed @Ron how to do the numpy approach so he’s set now.