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acil-bwh / SlicerCIP

Slicer extension for the Chest Imaging Platform
BSD 3-Clause "New" or "Revised" License
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Editing Automated Lung segmentation and then running parenchyma analysis on it #44

Open elomeiris opened 1 week ago

elomeiris commented 1 week ago

Hello, I am working on a project involving lung segmentation and volumetry in pediatric population. I am using the chest imaging platform extension to generate segmentation using parenchyma analysis tool in it, but as the segmentations are not always accurate, I need a way to manually edit them. I tried switching to segment editor (this used to work on previous 3Dslicer version like 4.10.2) but the segment don't transfer on the image when I switch to segment editor now on 3D slicer5.6.2. I was not able to switch to segment editor and edit those maps unless I save the data and then upload the CT again and the lung map (upload as segmentation). I believe that when I am transforming the "partialLungLabelMap" into a segmentation, I am losing the labels of all the lobes. CIP labels each color with a name - red for RUL, blue for RML, etc. When I transform it into a segmentation, 3Dslicer changes the labels of the color to the default labels the software uses. For example, red is RUL for CIP, but for 3DSlicer is the Precentral gyrus.

When I tried to run the parenchyma analysis on an edited segmentation it says "must contain segments right lung left lung other" because 3Dslicer replaced those color and their labels for the one the software uses by default. And then Parenchymal analysis doesn't recognize those new labels, and it will not run.

I tried to rename the segmentation manually, but it crashed when I ran CIP with the new labels or gave me the error again. Can you show me how I can I edit the segmentation map without error? What would be the easiest way? thumbnail_image

lassoan commented 1 week ago

Can you run Parenchyma Analysis using LungCTAnalyzer extension as shown here: https://discourse.slicer.org/t/parenchyma-analysis/25132/2?u=lassoan ?

elomeiris commented 1 week ago

Can you run Parenchyma Analysis using LungCTAnalyzer extension as shown here: https://discourse.slicer.org/t/parenchyma-analysis/25132/2?u=lassoan ?

Hi Yes I am able to do that but the segmentation is not accurate, it is catching heart contour and other structures that's why after running this parenchyma analysis I'd like to know if there s a way for me to manually fix the segments (exclude heart contours etc) and then run the lung parenchyma analysis again with the edited segmentation and get a table with the new more accurate values. Is there a way to do that ?

lassoan commented 1 week ago

@rbumm can you help with this question?

rbumm commented 1 day ago

Hi Yes I am able to do that but the segmentation is not accurate, it is catching heart contour and other structures that's why after running this parenchyma analysis I'd like to know if there s a way for me to manually fix the segments (exclude heart contours etc)

Hi, could you post an image that shows the parts that you do not want? and the names of the segmentations?