Various TCIA issues

[justin.kirby@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.7.dev202305042315 (2023-05-04 23:15:52 UTC)
Description
I downloaded some data from TCIA from CT Lymph Node collection.  Both the CT and SEG data load without crashing now, but the SEG doesn't look like it's overlaying the CT properly and once I started rotating the image around I somehow managed to move the location of the lymph node segmentation separately from the CT which definitely changed their alignment.  Finally, (this is likely just me being dense) I can't figure out if the CT is loading properly.  It should be a stack of 735 slices but it appears like a single slice is all I can view and it's trying to render that one slice into a 3d model.  How do I scroll through the stack of images if this isn't a bug?  I'm attaching a screenshot of the SEG label showing up outside of the body after doing some rotations.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.dev202305042315 (2023-05-04)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 61.7.259229997858724420813408711235467205350 format dicom fromDatabase
> tcia

Summary of feedback from opening 61.7.259229997858724420813408711235467205350
fetched from tcia  
---  
warnings | SeriesNumber not specified; setting to 0  
SeriesNumber not specified; setting to 0  
SeriesNumber not specified; setting to 0  
note | Opened 0 CT (abdominal_lymph_nodes) as #1.1.1, grid size 512,512,636,
pixel 0.684,0.684,0.325, shown at step 1, values int16  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> close session

> ui tool show "Download DICOM"

> open 61.7.136109627500567814530333386506613155124 fromDatabase tcia format
> dicom

Summary of feedback from opening 61.7.136109627500567814530333386506613155124
fetched from tcia  
---  
warnings | SeriesNumber not specified; setting to 0  
SeriesNumber not specified; setting to 0  
SeriesNumber not specified; setting to 0  
note | Opened 0 CT (abdominal_lymph_nodes) as #1.1.1, grid size 512,512,735,
pixel 0.84,0.84,0.683, shown at step 1, values int16  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> open 1.2.276.0.7230010.3.1.3.0.21117.1674505891.546546 fromDatabase tcia
> format dicom

Summary of feedback from opening
1.2.276.0.7230010.3.1.3.0.21117.1674505891.546546 fetched from tcia  
---  
warnings | Merged incoming unique studies with existing patient with same ID  
SeriesNumber not specified; setting to 0  
note | Opened 300 SEG (Lymph node segmentations) as #1.1.2, grid size
512,512,121, pixel 0.84,0.84,1.63, shown at step 1, values uint8  
  
Images from TCIA may be rotated so that flat planes appear invisible. If the
screen looks black but no error message has been issued, try rotating the
model into view with your mouse.  

> hide #!1.1.2 models

> show #!1.1.2 models

> hide #!1.1.2 models

> show #!1.1.2 models

> hide #!1.1.2 models

> show #!1.1.2 models

> hide #!1.1.2 models

> show #!1.1.2 models

> hide #!1.1.2 models

> show #!1.1.2 models




OpenGL version: 3.3.0 - Build 27.20.100.9749
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 7420
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,888,762,368
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz
OSLanguage: en-US

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File attachment: chimerax.png

chimerax.png​

[justin.kirby@…]

Added by email2trac

[Zach Pearson]

We initially render a slice but a dropdown menu on the Volume Viewer (this tool pops up on the lower right hand side of the screen) will let you pick between slices, orthoplanes, a volume, or a 3D surface. Switching the rendering to the 3D surface shows the segmentations are mostly within the 3D model but the slice ordering makes the model incoherent. This is a new edge case for how we determine slice ordering!

[Zach Pearson]

I've fixed the slice ordering and modified the code so that SEG images open as surfaces by default. I can see that the SEG image and the CT have different dimensions along one of the axes so the SEG is slightly below the CT. I'll see how other viewers display them to figure out what's up.

[Zach Pearson]

The SEG and CT should be aligned in today's builds.