View Issue Details
ID | Project | Category | View Status | Date Submitted | Last Update |
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0003857 | Slicer4 | Core: Diffusion and Tractography (Any modules) | public | 2014-09-23 09:10 | 2016-02-29 14:04 |
Reporter | lauren | Assigned To | alexy | ||
Priority | normal | Severity | major | Reproducibility | always |
Status | closed | Resolution | fixed | ||
Product Version | Slicer 4.3.1 | ||||
Target Version | Slicer 4.5.0-1 | Fixed in Version | Slicer 4.5.0-1 | ||
Summary | 0003857: 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 | ||||
Tags | No tags attached. | ||||
2014-09-23 09:11
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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. |
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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). 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 |
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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 |
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I am testing with today's nightly (Slicer 4.4.0 2015-03-25).
I tested this with single-tensor tracts generated by 3D Slicer. |
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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).
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Added support for Parallel and Perpendicular Diffusivity. |
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Fixed display of scalars on Fibers. |
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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) |
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I'm testing this again with the most recent nightly (06/17/15). Testing for interactive seeding:
Testing for label map seeding:
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Fixed parallel/perpendicular diffusivity on glyphs. Fixed interactive seeding line display. Jessica, please re-test in tomorrow's nightly. |
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All the tensor properties for lines, tubes, and glyphs work for both types of seeding |
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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: 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. |
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Fixed scalar display widget logic. |
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Tested, looks good. Thanks! |
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Closing. Tested by Isaiah. |
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Date Modified | Username | Field | Change |
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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) |