Hello. I would like to ask, in image segmentation, when we have already the predicted mask and we want to correct it.What is the way to remove parts of the mask or add some parts(painting) to the already masks? without paint them from the start,but use the predicted.So just work on the mask with add…

You can use Segment editor module for this. See tutorials here .

Thank you very much for your time:) I mean that we have an MRI image like this [image] (this is a polysistic kydney) and the mask for the kydney, that our model has predicted. Now we want to open them in slicer and edit this mask(just cutting and adding parts to the mask to make it fit better) and…

so, is there a way to load the predicted masks as “masks” and not just series of slices, so that the slicer recognize that they are masks and let us modify them (in the way that it would let us if we have made the mask manualy in slicer)? The files are dicom.

Segment Editor can edit data that has the type “segmentation” in Slicer. If you load a mask, then it’s most probably a volume node. First, you need to make sure it’s a labelmap. In the loading screen if you open the options part, there will be a checkbox for loading it as labelmap. Alternatively you…

Thank you for your time!!! I solved it like this, I uploaded the mask and the series(image MRI) and the problem was that it didnt recognize mask so I could not modify it. So these was the steps if someone is interested too load serie-load mask -go to volumes select mask convert to scalar volume g…

@Christineseven , If you have to do this for many patients, you can optionally also check out CaseIterator (in the extension manager under “utility”). I wrote this module to easily review a batch of cases, including reviewing (i.e. loading, adapting and saving under a new name) of segmentations. It …

Hi! I followed your instructions and could properly edit the mask, but how should I save it in order to use it as a mask? I tried saving the segmentation (in nifti and in nrrd), but it was probably in the wrong “format”. I couldn’t use it for freesurfer. Thanks a lot!

This last question was also posted and got answered here: [image] How to save brain structural edited masks (segment edited) in nifti for freesurfer use? Support Hi! I automatically generated structural brain masks with the purpose of using FreeSurfer. The masks need some…

Edit existing segmentation

Support

lassoan (Andras Lasso) July 2, 2021, 5:10am 11

This last question was also posted and got answered here:

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Edit existing segmentation

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