View Issue Details

IDProjectCategoryView StatusLast Update
0001612Slicer4Module VolumeRenderingpublic2012-08-21 09:48
Reporterkikinis Assigned Tofinetjul  
PrioritynormalSeverityminorReproducibilityalways
Status closedResolutionfixed 
PlatformMACOSOS XOS Version10.7.2
Product Version 
Target VersionSlicer 4.1.0Fixed in VersionSlicer 4.1.0 
Summary0001612: initial transfer function looks weird
Description

load ct, select body ct preset, go to volume rendering module and render with the defaults. See attached screenshot. Compare to the appearance with the same workflow in slicer 3

TagsNo tags attached.

Activities

2011-12-06 02:40

 

2011-12-06 02:44

 

kikinis

kikinis

2011-12-06 02:45

developer   ~0003419

Slicer 3 achieves a more pleasing result with the same workflow. The transfer function makes more sense.

finetjul

finetjul

2012-02-22 12:29

administrator   ~0003693

Fixed in r19343:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19343

kikinis

kikinis

2012-02-23 00:55

developer   ~0003701

thank you, thank you

kikinis

kikinis

2012-03-04 11:42

developer   ~0003777

Unfortunately, the specifics are not quite right. I used the sample data set CTA-cardio on mac nightly march 4:
min -322 max 689

2012-03-04 11:42

 

WhatIget.png (524,702 bytes)
WhatIget.png (524,702 bytes)

2012-03-04 11:43

 

WhatIshouldGet.png (301,387 bytes)
WhatIshouldGet.png (301,387 bytes)
kikinis

kikinis

2012-03-04 11:44

developer   ~0003778

"What I get" shows that the ramp is not positioned properly. "What I should get" shows a ramp which I adjusted manually to the correct beginning and end.

finetjul

finetjul

2012-03-08 12:45

administrator   ~0003812

Slicer3:
Go to Volumes module and Select CT Abdomen preset
WL: -135Min 215Max (350W 40L)
Threshold: -959Min 3532Max
Go to Volume Rendering module:
Color map: -135Min 215Max
Opacity map: -135Min 215Max -> not consistent with Threshold
Synchronize with Volumes:
Color map: -135Min 215Max
Opacity map: -959Min -954Max -> inconsistent with first values when opening volume rendering, it is very confusing.

Slicer4:
Go to Volumes module and Select CT Abdomen preset
WL: -135Min 215Max (350W 40L)
Threshold: -1024Min 3532Max -> it should be -959Min, I'll fix it
Go to Volume Rendering module:
Color map: -135Min 215Max
Opacity map: -1024Min 3532Max -> consistent with Threshold
Synchronize with Volumes:
Color map: -135Min 215Max
Opacity map: -1024Min 3532Max -> still consistent

The problem with the initial values in Volume Rendering in Slicer3 are not consistent.
In addition, once the transfer functions are set, there is no way to go back to those values, it's a one time shot.
It really is confusing to me.

Alternative suggestions (not orthogonal):
Presets in Volumes module can set Threshold values. CT-Abdomen sets WL and Threhsold to -135Min, 215Max (effort index: 1)
Add Threshold mode in Volumes module to "follow Window/Level" and make it the default (effort index: 2)

kikinis

kikinis

2012-03-08 22:33

developer   ~0003818

It worked properly in Slicer 3. I just want back what I already had in Slicer 3, No more, no less.

liuy5

liuy5

2012-03-09 04:50

developer   ~0003819

Difference I have found between Slicer 3 and Slicer 4:

In Slicer 3, Volumes module display settings will not be used by volume rendering unless "Sync with volumes" button clicked. Whereas, in Slicer 4, volumes module display settings will be used as default for volume rendering. What Ron seen in Slicer 3 is volume rendering done with its own opacity ramp (SetupVolumePropertyFromImageData()), whereas in Slicer 4 the opacity ramp is generated based on volumes module (UpdateDisplayNodeFromVolumeNode() called in createVolumeRenderingDisplayNode).

Another issue I found is that sometimes VolumeRendering shows complete dark renderings. But any update to 3D view will revert it back to normal rendering. That's probably why Ron is seeing dark images

finetjul

finetjul

2012-03-09 04:55

administrator   ~0003820

I understand, and I will do it.
Now, going further, how do you display a 2D slice in 3D view with the air transparent ?
You first show the 2D slice in 3D, go to Volumes, select CT-Abdomen preset, and you need to play with the threshold slider all the way to ~ -135.
Question: wouldn't it be nice (meaningful) if it was already at -135 for you ?
The min of the window/level is likely to be the min of the threshold.
If you believe though, then it makes the initial look in Volume Rendering the same as in Slicer3 and it is the same look when "Follow Volume" is ON.

liuy5

liuy5

2012-03-09 05:02

developer   ~0003821

I like the idea of "The min of the window/level is likely to be the min of the threshold.". Would it be possible to added a "Follow W/L" item in the combo box showing "Off", "Auto", and "Manual" so that user can apply W/L setting to thresholding?

finetjul

finetjul

2012-03-12 12:53

administrator   ~0003843

Fixed in r19573:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19573

kikinis

kikinis

2012-03-21 07:41

developer   ~0003906

The rendering now looks good. The scalar opacity map: the chart does not look correct. See most recent image.

2012-03-21 07:42

 

Issue History

Date Modified Username Field Change
2011-12-06 02:40 kikinis New Issue
2011-12-06 02:40 kikinis Status new => assigned
2011-12-06 02:40 kikinis Assigned To => finetjul
2011-12-06 02:40 kikinis File Added: Screen Shot 2011-12-06 at 7.36.40 AM.png
2011-12-06 02:44 kikinis File Added: Screen Shot 2011-12-06 at 7.43.44 AM.png
2011-12-06 02:45 kikinis Note Added: 0003419
2012-02-22 12:29 finetjul Note Added: 0003693
2012-02-22 12:29 finetjul Status assigned => resolved
2012-02-22 12:29 finetjul Fixed in Version => Slicer 4.1.0
2012-02-22 12:29 finetjul Resolution open => fixed
2012-02-23 00:55 kikinis Note Added: 0003701
2012-02-23 00:55 kikinis Status resolved => closed
2012-03-04 11:42 kikinis Note Added: 0003777
2012-03-04 11:42 kikinis Status closed => feedback
2012-03-04 11:42 kikinis Resolution fixed => reopened
2012-03-04 11:42 kikinis File Added: WhatIget.png
2012-03-04 11:43 kikinis File Added: WhatIshouldGet.png
2012-03-04 11:44 kikinis Note Added: 0003778
2012-03-08 12:45 finetjul Note Added: 0003812
2012-03-08 22:33 kikinis Note Added: 0003818
2012-03-09 04:50 liuy5 Note Added: 0003819
2012-03-09 04:55 finetjul Note Added: 0003820
2012-03-09 05:02 liuy5 Note Added: 0003821
2012-03-12 12:53 finetjul Note Added: 0003843
2012-03-12 12:53 finetjul Status feedback => resolved
2012-03-12 12:53 finetjul Resolution reopened => fixed
2012-03-21 07:41 kikinis Note Added: 0003906
2012-03-21 07:41 kikinis Status resolved => feedback
2012-03-21 07:41 kikinis Resolution fixed => reopened
2012-03-21 07:42 kikinis File Added: RenderingGood-TransferfunctionBad.png
2012-08-01 04:25 kikinis Status feedback => resolved
2012-08-01 04:25 kikinis Resolution reopened => fixed
2012-08-01 04:39 kikinis Status resolved => closed
2012-08-21 09:48 jcfr Target Version => Slicer 4.1.0