File edited in preview version 4.11.0 now lacks all segments. Please help!

Support
1

Operating system: OS X
Slicer version: 4.11.0
Expected behavior: I was using the stable version of Slicer (4.10.2) to annotate an MRI brain (months of work) but the paint tool was very laggy, so I downloaded the preview version 4.11.0 to see if it improved things. Once it seemed to be working well, I saved the file, hoping to eventually return to editing it with the stable version since I am collaborating with others who use the stable version.

Actual behavior: However, now when I open the mrml file in the stable 4.10.2 release, all of the segments are missing except for 1 of them. If I go to Data, I can see that the segments are there, but they don’t show up in the Segment Editor. I see the same thing if I open this file on a different computer, so somehow the file has been saved differently using 4.11.0, so it no longer displays the information correctly on 4.10.2.

I’d really appreciate any help getting my file to display correctly in the stable version 4.10.2. It seems like there is a bug in the preview version of slicer with how it saves files.

2

Scenes that you save in a Slicer version are only guaranteed to work in that version or later versions. You can of course still save data in a format that is compatible with older versions.

For example, you can export segmentation to a labelmap node and you can load that labelmap into Slicer-4.10.2 and convert it to segmntation. However, since infrastructure so dramatically improved since Slicer-4.10.2, if you do a lot of segmentations, I would recommend to upgrade to a recent Slicer-4.11 version.

3

Thank you for the response. I’m afraid I’m not very experienced with 3D Slicer and I’m failing to get this to work.

In version 4.11.0 I went to > Segmentations > Export/import models and labelmaps

  • Export
  • Labelmap
  • Export to new labelmap

Advanced

  • All exported segments
  • my reference volume

Export to files

  • STL
  • Scale 1.00
  • Coordinate system LPS
    Export

Now in Version 4.10.2 I add the original MR data (.nii.gz) (“volume”) and I add the labelmaps (.stl) (“model”).

To convert the labelmaps to segments I go to > Data

  • right click on one of the labelmaps
  • select “convert model to segmentation node”

However, the label maps don’t seem to have preserved their positioning/scale on the original map, so when I view the data in Four-up and toggle slice visibility in 3D view, the labelmaps are not overlaid on the 3D volume and the scale is wrong.

How do I save the labelmaps so that they preserve their position and size?

thank you very much

4

I would not recommend to export segmentation as STL, as it is a lossy storage format for segmentations created by Segment Editor (which uses binary labelmap representation). Instead:

Simple export/import:

  • In Slicer Preview Release: right-lick on the segmentation in Data module and choose “Export visible segments to binary labelmap”
  • In old Slicer release: load the segmentation file by drag-and-dropping to application window and clicking OK

Export/import with preserving colors:

  • In Slicer Preview Release:
    • right-lick on the segmentation in Data module and choose “Export visible segments to binary labelmap”
    • save the exported labelmap and the corresponding color table (.nrrd and .ctbl file)
  • In old Slicer release:
    • load the color table file by drag-and-dropping to application window and clicking OK
    • load the segmentation file by drag-and-dropping to application window, check “Show options”, scroll to the right, and select the color table that you loaded (at the bottom of the list) and clicking OK
5

Ah ok thank you. The only thing is when I do that the segmentations are a single file, and they’re not aligned on the original volume and editable like they were in the original version (or on 4.11.0). I think I solved the issue a different way:

  • the alignment was fixed by changing the coordinate system to RAS when I exported the segments to labelmaps

  • I imported the labelmaps as segments (quicker than my method above):

Add data > choose file

  • change “model” to “segmentation”

  • once I had imported all of the segmentations they were each in separate segmentations rather than as options under a single “Segmentation”. To solve this I did:

Segmentations
Active segmentation - “add new segmentation” - name it “Segmentation”
copy/move segments

  • select each segment from the dropdown menu, click on it, then use <+ to add it to Segmentation
  • once all of the segments have been added go to > Data. All of the segments should be under “Segmentations” so delete the individual files.
  • to edit them, go to Segment editor, change “Segmentation : Segmentation”, and select your master volume. Then select a segment to edit and say yes to converting to binary map

The disadvantage here is you have to recolor all of the segments yourself.

Thanks for your help!

6

For segments edited in Segment Editor, you lose details if you export them to STL and then import them. For this reason alone, I would strongly recommend exporting to labelmap.

7

Ah yes, I see what you mean.

Great that worked, thank you!

For anyone else that has this problem, after following your instructions to load the color map and segmentation file, you go to > Data then right-click on Segmentation-label > convert labelmap to segmentation node, and everything is restored.

Thanks again!

1 Like