View Issue Details
ID | Project | Category | View Status | Date Submitted | Last Update |
---|---|---|---|---|---|
0003855 | Slicer4 | Core: Diffusion and Tractography (Any modules) | public | 2014-09-23 08:54 | 2018-03-02 11:06 |
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 | 0003855: The output baseline volume is not the baseline volume | ||||
Description | The DiffusionWeightedVolumeMasking module outputs a mask volume and another volume, which it calls the Baseline Volume. This output is not a baseline. It is apparently the average of the diffusion-weighted images. Signal is low in the ventricles, due to diffusion. See screenshots. Note that the DWI to DTI estimation produces a Baseline Volume that is, in fact, the baseline. This image is not sensitized to diffusion (the definition of the baseline), therefore signal is high in the ventricles. | ||||
Tags | No tags attached. | ||||
2014-09-23 08:54
|
|
2014-09-23 08:54
|
|
Now the output has changed but it is still not a baseline image. The images attached show the new output, some sort of a thresholded image that was probably used in mask computation. For reference the actual baseline (from when tensors were computed) is the second screenshot. |
|
2014-12-17 15:12
|
|
2014-12-17 15:12
|
|
Fixed in r24673 Thanks to "Orjan Bergmann", the issue is now fixed and the outputs (baseline and mask) of the modules are now tested for regression. Bonus: It would be great to add an other test checking if the "removeisland" functionality work as expected. Name of the test would be "DiffusionWeightedVolumeMaskingTest_removeisland" For reference, here is the commit message: //---------------------- The updated line calculates the magnitude of each gradient, and The use of "abs()" on double values caused the magnitude to This commit fixes the incorrect logic using "fabs()", simplifies the test Note that the "--removeislands" should be tested in a separate test case. Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> From: Orjan Bergmann <orjan.bergmann@gmail.com> |
|
Date Modified | Username | Field | Change |
---|---|---|---|
2014-09-23 08:54 | lauren | New Issue | |
2014-09-23 08:54 | lauren | Status | new => assigned |
2014-09-23 08:54 | lauren | Assigned To | => alexy |
2014-09-23 08:54 | lauren | File Added: Incorrect_Baseline_From_Masking.png | |
2014-09-23 08:54 | lauren | File Added: Correct_Baseline_From_DTI_calc.png | |
2014-12-17 15:11 | lauren | Note Added: 0012793 | |
2014-12-17 15:12 | lauren | File Added: still_not_baseline_but_different.png | |
2014-12-17 15:12 | lauren | File Added: this_is_what_the_baseline_should_look_like.png | |
2015-10-28 20:56 | jcfr | Target Version | => Slicer 4.5.0-1 |
2015-10-28 20:57 | jcfr | Note Added: 0013465 | |
2015-10-28 20:57 | jcfr | Status | assigned => resolved |
2015-10-28 20:57 | jcfr | Fixed in Version | => Slicer 4.5.0-1 |
2015-10-28 20:57 | jcfr | Resolution | open => fixed |
2016-02-29 13:58 | jcfr | Category | Module DiffusionWeightedVolumeMasking => 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) |
2018-03-02 11:06 | jcfr | Status | resolved => closed |