View Issue Details

IDProjectCategoryView StatusLast Update
0003857Slicer4Core: Diffusion and Tractography (Any modules)public2016-02-29 14:04
Reporterlauren Assigned Toalexy  
PrioritynormalSeveritymajorReproducibilityalways
Status closedResolutionfixed 
Product VersionSlicer 4.3.1 
Target VersionSlicer 4.5.0-1Fixed in VersionSlicer 4.5.0-1 
Summary0003857: Scalar display is incorrect in Tractography Display
Description

The only thing that can be correctly displayed on Tubes is FractionalAnisotropy, ColorOrientation, and LinearMeasure.

All others are broken.

Scalars with units of diffusivity (Trace, eigenvalue measures, perpendicular and parallel diffusivities) require a scalar range update in order to display them. However, the scalar range stays from 0..1.

Other values that should be in the range 0..1 (Planar and Spherical Measures) do not display, so it is likely their pipeline is hooked up incorrectly.

Additional Information

Please see screenshots and test dataset.

TEST DATA: https://www.dropbox.com/s/norftqveoclwg5n/1224_wb_default_selected.vtk?dl=0

TagsNo tags attached.

Activities

2014-09-23 09:11

 

2014-09-23 09:11

 

2014-09-23 09:11

 

2014-09-23 09:11

 

2014-09-23 09:12

 

2014-09-23 09:12

 

2014-09-23 09:12

 

2014-09-23 09:13

 

2014-09-23 09:13

 

2014-09-23 09:13

 

2014-09-23 09:13

 

lauren

lauren

2014-09-23 09:15

developer   ~0012585

The scalar display is also broken for lines and glyphs, so whatever fixes are needed should be put there too. In the screenshots, the solid color red or white tubes are all incorrect. The ones where there are colors shown are correct, hopefully.

lauren

lauren

2014-12-02 09:33

developer   ~0012750

I have tested this again with the latest nightly version Dec 2, and the issues are still present. Here is a summary of the current state (not exhaustive as I did not re-test every available parameter)

These issues are all present with lines and tubes. Glyphs are similar but worse (see below).
a) When I switch from tensor1 FA to tensor2 FA the view does not change.
b) When I color tube by saved scalar value FA1 and FA2, it is just red. The auto w/l updates, though
c) I can see saved scalar values of Trace1 and Trace2 but not FA1/2. LUT issue?
d) in Tensor Property, FA and LinearMeasure appear to work. Trace and PlanarMeasure are all red.

Glyphs have the above issues, plus none of the stored scalar values (not even trace) can be viewed.

NEW TEST DATA with tensors along tracts can be found here. Load the MRML file from this directory, or alternatively just load one of the VTP files. https://www.dropbox.com/sh/8ejckahq57k9bda/AABY8Ce_FJZ3b59IGzXiBg5ma?dl=0

alexy

alexy

2015-03-24 13:56

developer   ~0012983

I have fixed displaying of Tensor properties and their ranges in Tractography display module for lines/tubes/glyphs. Lauren please test.

However, "Scalar Value" display is still broken, it seems the issue is in ModelsDisplayableManager class.

At revision: 24099

lauren

lauren

2015-03-26 11:19

developer   ~0012987

I am testing with today's nightly (Slicer 4.4.0 2015-03-25).

  1. When I first go to advanced display and change Tensorp Property, nothing changes in the 3D window (no render).

  2. Then I click the eye on and off once to toggle visibility, and the menu will now cause updates.

  3. On the Line display, Trace works and the W/L updates to show it. On the Tubes display, the Trace does not work (it stays cyan always and W/L does not update).

  4. On Lines, Parallel and Perpendicular Diffusivity do not work. They are always red and the W/L does not update.

  5. On Tubes, all of Trace, the diffusivities, and the eigenvalues are broken. They are cyan always.

  6. Glyphs appear to perform just as lines, where all measures seem to work except for Parallel and Perpendicular Diffiusivity.

I tested this with single-tensor tracts generated by 3D Slicer.

alexy

alexy

2015-03-27 10:21

developer   ~0012988

I cannot reproduce this behavior (0000001 and 0000002). Are you sure you are using the correct tab in the Advanced Display? The fiber are loaded as lines, but the default tab in display is Tubes, you have to switch to Lines first, so may be that what is causing the confusion (I get confused by this every time, but that was how Ron wanted it since the seeding modules produce tubes).

  1. I have found and fixed the problem for Tubes (in tomorrow's nightly). They should work in the same way as Lines now.

  2. The Parallel and Perpendicular Diffusivity are not implemented in the vtkPolyDataTensorToColor class. I don't know the math for it, so if somebody tells me that (or just edit the slicer code) we can unable this. Alternatively we can remove these options from UI.

  3. I have found and fixed the problem for Tubes (in tomorrow's nightly). They should work in the same way as Lines now.

  4. See my comments on # 4

alexy

alexy

2015-05-26 07:51

developer   ~0013101

Added support for Parallel and Perpendicular Diffusivity.
At revision: 24273

alexy

alexy

2015-06-13 14:18

developer   ~0013125

Fixed display of scalars on Fibers.
Completed: At revision: 24307

jessicalee8140

jessicalee8140

2015-06-18 08:40

reporter   ~0013136

I'm testing the advanced tractography display with the (06/13/2015) nightly.

I tested it with both label map seeding and interactive seeding.

For label map seeding, the tractography display works for lines and tubes for every tensor property. But for gylphs, it doesn't work for parallel diffusivity and perpendicular diffusivity (they appear red)

For interactive seeding, none of the tensor properties display on lines (they all appear white). This is not a updating issue, because even after switching to another setting and going back, the tensors still do not display. All the tensor properties appear correctly on tubes. On glyphs, everything appears correctly except for parallel diffusivity and perpendicular diffusivity (appears red)

jessicalee8140

jessicalee8140

2015-06-18 10:00

reporter   ~0013137

I'm testing this again with the most recent nightly (06/17/15).

Testing for interactive seeding:

  1. There are updating issues for the lines display. When it is initially selected, all tracts appear white. But when I clicked on "color fibers by mean orientation" and back to "of tensor property", the tracts displayed properly with colors for every tensor property.

  2. Everything in the tubes setting displays properly.

  3. Glyphs displays everything properly except for parallel and perpendicular diffusivity. (Glyphs appear red)

Testing for label map seeding:

  1. Before using the tractography display module, I used both label map and interactive seeding and used tractography display to view each of them separately. I viewed interactive seeding first. Under the "simple display" tab, when I switched fiber bundles to look at to the label map tractography, the visibility option under advanced display does not default to on, so the main display shows the last viewed tract.

  2. All the tensors display properly on lines and tubes.

  3. Parallel and perpendicular diffusivity do not display correctly on glyphs, and appear red.

alexy

alexy

2015-06-19 08:01

developer   ~0013139

Fixed parallel/perpendicular diffusivity on glyphs. Fixed interactive seeding line display.

Jessica, please re-test in tomorrow's nightly.

jessicalee8140

jessicalee8140

2015-06-21 08:37

reporter   ~0013143

All the tensor properties for lines, tubes, and glyphs work for both types of seeding

lauren

lauren

2015-11-02 10:45

developer   ~0013492

Unfortunately this is still broken but now in a different way. When one fiber bundle is active, it is possible to display its tensor properties and also scalar values along the tracts. But when the user selects another active fiber bundle, the first one reverts to some default setting, which is whatever was displayed initially when it was loaded, apparently. This means the module is not useable for more than one fiber tract.

Steps to reproduce:
1) Load two fiber bundles.

2) Select any tensor property or scalar value on fiber bundle one.

3) Then select fiber bundle 2 in the interface. Fiber bundle one will revert to displaying something else.

alexy

alexy

2015-11-07 06:54

developer   ~0013568

Fixed scalar display widget logic.
At revision: 24706

inorton

inorton

2015-11-09 06:45

developer   ~0013575

Tested, looks good. Thanks!

jcfr

jcfr

2015-11-10 14:40

administrator   ~0013584

Closing. Tested by Isaiah.

Issue History

Date Modified Username Field Change
2014-09-23 09:10 lauren New Issue
2014-09-23 09:10 lauren Status new => assigned
2014-09-23 09:10 lauren Assigned To => jcfr
2014-09-23 09:11 lauren File Added: Screenshot 2014-09-23 12.49.27.png
2014-09-23 09:11 lauren File Added: Screenshot 2014-09-23 12.49.43.png
2014-09-23 09:11 lauren File Added: Screenshot 2014-09-23 12.50.05.png
2014-09-23 09:11 lauren File Added: Screenshot 2014-09-23 12.50.13.png
2014-09-23 09:12 lauren File Added: Screenshot 2014-09-23 12.50.24.png
2014-09-23 09:12 lauren File Added: Screenshot 2014-09-23 12.50.33.png
2014-09-23 09:12 lauren File Added: Screenshot 2014-09-23 12.50.42.png
2014-09-23 09:13 lauren File Added: Screenshot 2014-09-23 12.50.49.png
2014-09-23 09:13 lauren File Added: Screenshot 2014-09-23 12.52.13.png
2014-09-23 09:13 lauren File Added: Screenshot 2014-09-23 12.52.21.png
2014-09-23 09:13 lauren File Added: Screenshot 2014-09-23 12.52.36.png
2014-09-23 09:15 lauren Note Added: 0012585
2014-09-23 09:53 jcfr Assigned To jcfr => alexy
2014-09-23 09:53 jcfr Category Core: Base Code => Module TractographyDisplay
2014-09-23 09:53 jcfr Target Version => Slicer 4.4.1
2014-12-02 09:33 lauren Note Added: 0012750
2015-03-24 13:56 alexy Note Added: 0012983
2015-03-24 13:57 alexy Status assigned => feedback
2015-03-26 11:19 lauren Note Added: 0012987
2015-03-27 10:21 alexy Note Added: 0012988
2015-05-26 07:51 alexy Note Added: 0013101
2015-06-13 14:18 alexy Note Added: 0013125
2015-06-13 14:18 alexy Status feedback => resolved
2015-06-13 14:18 alexy Resolution open => fixed
2015-06-16 17:27 alexy Status resolved => feedback
2015-06-16 17:27 alexy Resolution fixed => open
2015-06-18 08:40 jessicalee8140 Note Added: 0013136
2015-06-18 10:00 jessicalee8140 Note Added: 0013137
2015-06-19 08:01 alexy Note Added: 0013139
2015-06-21 08:37 jessicalee8140 Note Added: 0013143
2015-09-09 08:29 jcfr Target Version Slicer 4.4.1 => Slicer 4.5.0-1
2015-11-02 10:45 lauren Note Added: 0013492
2015-11-07 06:54 alexy Note Added: 0013568
2015-11-07 06:54 alexy Status feedback => resolved
2015-11-07 06:54 alexy Resolution open => fixed
2015-11-09 06:45 inorton Note Added: 0013575
2015-11-10 14:40 jcfr Note Added: 0013584
2015-11-10 14:40 jcfr Status resolved => closed
2015-11-10 14:40 jcfr Fixed in Version => Slicer 4.5.0-1
2015-11-30 17:50 jcfr Category Module TractographyDisplay => Module: Any Tractography modules
2016-02-29 14:04 jcfr Category Module Tractography (any modules) => Core: Diffusion & Tractography
2016-02-29 14:05 jcfr Category Core: Diffusion & Tractography => Core: Diffusion & Tractography (Any modules)
2016-06-20 14:14 jcfr Category Core: Diffusion & Tractography (Any modules) => Core: Diffusion and Tractography (Any modules)