I have a T1 volume and a segmented volume with ventricles , tumor and blood vessels ,I am trying to get a figure like this one ,this is taken from a paper.
This is a feature that hasn’t been merged into Slicer yet (ENH: Add connector line for fiducial markup label texts by lassoan · Pull Request #6809 · Slicer/Slicer · GitHub).
When functional, you can generate figures like this;
Until then, I think your best option is to get screenshot and add those texts and lines in Illustrator and/or powerpoint. That will give you more flexibility in terms of colors/font choices as well…
@mukund_shah if you want to display the ventricle, tumor, and blood vessels then you can use the Segment Editor. The Neurosurgical planning tutorial is a good starting point.
But i already have a segmented label volume with ventricles,tumor and blood vessels along with T1 volume do I still need segment editor?
Not at all, then you are done. You can segment the brain surface using HDBet or SwissSkullStripper and display the structures that you already segmented. You can adjust the transparency of both the brain and the segmentations. You can draw the trajectories as curves in Markups module.
@lassoan i am getting brain output after skull striping ,how do I change opacity of this? i cant see any option here for changing that
You have rendered the mask. Instead, render the skull-stripped image instead. You can adjust opacity of volume rendering by decreasing the opacity values in the Scalar Opacity Mapping function.
@lassoan thanks to you i am able to make this figure now, one last thing how can I make these blood vessels etc more smooth looking as in the first image? mine look granular
If you load your image as a segmentation (in “Add data” popup window, choose “Segmentation” in the description column) then you get a lot more visualization options - smoothing, opacity, etc. You can also apply further smoothing, thickening, etc. in Segment Editor module.
For additional improvements in appearance, you can use Lights module in Sandbox extension. Especially “ambient shadows” may make a big difference.
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