Using Scissors to make mask on MRI

Hi all,

I’m trying to create a mask for registration of MRI and CT pelvis scans using scissors in segment editor. It works perfectly for CT but when I draw the same free-form area on the MRI the mask only goes half through the space that I drew as shown in the images. I tried other tools like draw and paint but they also can fill up to the lower half of the MRI scan and not the upper half. What can I do to solve this issue ? Thank you.
Screen Shot 2021-02-05 at 12.51.05 PM Screen Shot 2021-02-05 at 12.50.38 PM

You can paint up to the boundaries of the segmentation. See how to change that in the Segment Editor module documentation.

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Thanks for your reply. I want to feed the result of this registration with mask to the second round of registration to see if my result improves (with Elastix) but I don’t see a way to do this! I mean non of the parameter files have transformation information so that I can edit the files the same way. how do I do multiple registrations with Elastix in 3D slicer?

I’m not sure how exactly registration stages in Elastix pass on the transforms, you can ask it on Elastix or ITK forums.

If you want, you can run one registration phase at a time. First pass only a single parameter file to elastix, inspect the results, tune the parameters as needed. Then, run elastix again using the transformed (resampled) moving volume as input for this registration phase. Resample a volume several times is not ideal (each resampling is a lossy operation), so in the end it is better to concatenate all the transforms and apply it at once to the original moving volume.

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