Scene views color table storage nodes have incorrect path to the color table file:
<ColorTableStorage
id="vtkMRMLColorTableStorageNode23" name="vtkMRMLColorTableStorageNode23" hideFromEditors="true" selectable="true" selected="false" fileName="../__BundleSaveTemp-2012-10-04_19+01+34.531/Abdominal_Atlas_2012/Data/AbdominalAtlasColors.ctbl" useCompression="1" readState="0" writeState="0" ></ColorTableStorage>

trying to save a regular scene file first and then as an mrb...

Saving as mrml scene only, paths to color table are fine in scene views.
Then save as an mrb directly after, the paths point to the temporary directory.

Looks like all the storage nodes in the scene views are still pointing at the temp save dir for the bundle.
Maybe only the color nodes are trying to re-read themselves on scene view restore?

Alex is changing the root directory on the scene view nodes during an mrb save.

Set root directory in the scene view nodes when saving .MRB files.
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=21289

This fix doesn't seem to have helped all that much with the Brain Atlas file
http://slicer.kitware.com/midas3/download?items=10397

Granted, it was odd to begin with, but after opening the mrb and then saving it again, the top level scene view storage nodes have:
fileName="../../../__BundleLoadTemp2012-10-29_13+21+32.343/2012-09-18/
/Master%20Scene%20View1.png"
and
fileName="../../__BundleSaveTemp-2012-10-29_14+14+18.825/2012-10-29/projectsmarianna/ankara/tmp/ba-correction/AUG15/Left%20Cerebral%20Hemisphere.png

In the first scene view, volume storage nodes don't have the file list members reset:
fileName="Data/A1_grayT1.nrrd" fileListMember0="projectsbirn/nicole/Slicer42/Slicer4-SuperBuild-Debug/Slicer-build/tmpSlicer/__BundleSaveTemp-2012-10-29_14+14+18.825/2012-10-29/Data/A1_grayT1.nrrd"

and the color table storage node :
fileName="../../__BundleLoadTemp2012-10-30_14+01+05.118/2012-10-29/tmpSlicer/__BundleSaveTemp-2012-10-29_14+14+18.825/2012-10-29/projectsmarianna/ankara/tmp/ba-correction/AUG15/colorfiles/hncma-atlas-lut-mod2.ctbl"

Exiting Slicer and opening the newly saved mrb, all the scene view pngs are black because the thumbnail files weren't found. Restoring one scene view (Brainstem), looks mostly okay (color node is okay on the label map volume).

Will test with the abdomen atlas next.

Scene view pngs are missing when open the re-saved abdominal atlas mrb
http://slicer.kitware.com/midas3/download?items=8301

<SceneViewStorage
id="vtkMRMLSceneViewStorageNode2" name="SceneViewStorage_1" hideFromEditors="true" selectable="true" selected="false" fileName="../../__BundleLoadTemp2012-10-30_20+43+54.274/Abdominal_Atlas_2012/Data/Upper%20IG%20Tract.png" useCompression="1" readState="0" writeState="4" ></SceneViewStorage>

The data bundle png was fine.

Restoring the bone structures scene view, the segmentation volume has a black color table.

Nicole, does it happen when you start with a valid scene? Can you describe a scenario when you start with the valid scene and end up with invalid?

Fixed SceneViewStorage node's filename for MRB file.
revision: 21290

Nicole please test with starting with a valid scene file.

It has to work with the Abdominal, Brain and Knee atlas files.
The Abdominal at least has an updated mrml file, it was recreated recently from scratch.

Current state: the scene view pngs are now correct again, but the color table nodes in the scene views still have all black entries. The file paths in the mrml file are correct, so I'm digging in further.

If the bug fix is in the code that generates the scene, then I don't see how we can make the old scenes work.

Seems like the bug is in the color node copy right now. working on it.

Strongly suspect it's a scene view restore logic error that I made on commit 20932:
http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Libs/MRML/Core/vtkMRMLSceneViewNode.cxx?r1=20932&amp;r2=20931&amp;pathrev=20932
line 498: the nodes that need to have UpdateScene called on them are the ones that were no scene view nodes aka they were included in the scene view.

Fixing this is probably going to expose the fact that the color table storage node in the scene view at that point still points to the temporary bundle directory since it was updated on mrml scene read... testing...

I could reset the scene view storage node file names to be relative, but that's not going to fix the underlying problem that when reading in an mrb file, the dir where it was unpacked has been deleted - there are no files to re-read when restoring scene views.

Considering MRB/Sceneview are not required for RSNA and the tutorial, re-targeted for 4.2.1.

Seems that are still issue .. see http://na-mic.org/Bug/view.php?id=2512#c7257

Edited the mrml file to include the color file data in the mrml file rather than just in the color file. This fixed the missing color information in the scene views, but we still need to revisit mrb + deleting files + restoring scene views in general.
Upload to Midas, in Nightly:
http://slicer.kitware.com/midas3/download?items=10277
Abdominal_Atlas_2012.mrb
Upload to Midas in 4.2 (thisone has the item id used in the AtlasTests.py file):
http://slicer.kitware.com/midas3/download?items=8301

confirmed that download and run test shows proper colors in scene views.

Excellent.
Is there anything to update on the 4.2 branch ?

No update to the 4.2 branch needed, I uploaded a new revision of the mrb, the url didn't change.