From ac976c792b398204f8ce3b373c21ca501c466737 Mon Sep 17 00:00:00 2001 From: Andrey Fedorov Date: Thu, 1 Nov 2018 18:32:50 -0400 Subject: [PATCH] updates --- content/results/seg/brainlab.md | 76 ++++++++++++++++---------------- content/results/seg/epad.md | 43 ++++++------------ content/results/seg/index.md | 66 --------------------------- content/results/seg/slicer.md | 29 ++++++------ SUMMARY.md => gitbook/SUMMARY.md | 0 book.json => gitbook/book.json | 0 mkdocs.yml | 9 ++-- 7 files changed, 69 insertions(+), 154 deletions(-) rename SUMMARY.md => gitbook/SUMMARY.md (100%) rename book.json => gitbook/book.json (100%) diff --git a/content/results/seg/brainlab.md b/content/results/seg/brainlab.md index dd76844..7f1e60f 100644 --- a/content/results/seg/brainlab.md +++ b/content/results/seg/brainlab.md @@ -1,53 +1,52 @@ -# Brainlab -1.**Description of the platform/product**: + 1.**Description of the platform/product**: -* **name and version of the software**: Brainlab SmartBrush 2.5 and Brainlab SmartViewer 3.1; SmartViewer can only display DICOM SEG; SmartBrush can create SEG and display them, however SmartViewer displays them much better -* **free?** no -* **commercial?** yes -* **open source?** no -* **what DICOM library do you use?** [Merge DICOM Toolkit](http://www.merge.com/Solutions/Toolkits/Merge-DICOM-Toolkit.aspx), however the toolkit does not provide API for handling DICOM SEG objects, so all of the features related to handling DICOM SEG had to be implemented + * **name and version of the software**: Brainlab SmartBrush 2.5 and Brainlab SmartViewer 3.1; SmartViewer can only display DICOM SEG; SmartBrush can create SEG and display them, however SmartViewer displays them much better + * **free?** no + * **commercial?** yes + * **open source?** no + * **what DICOM library do you use?** [Merge DICOM Toolkit](http://www.merge.com/Solutions/Toolkits/Merge-DICOM-Toolkit.aspx), however the toolkit does not provide API for handling DICOM SEG objects, so all of the features related to handling DICOM SEG had to be implemented -2.**Description of the relevant features of the platform**: + 2.**Description of the relevant features of the platform**: -* **are both single and multiple segments supported?** Current version of Brainlab SmartBrush can write only single-segment objects, but reads both single- and multi-segment -* **how are the overlapping segments handled?** The user can see the outline of the contour \(the area inside the the contour is slightly color-washed\) -* **do you support both BINARY and FRACTIONAL segmentation types?** Brainlab always exports segmentations as FRACTIONAL type and RLE-compressed -* **do you render the segment using the color specified in the DICOM object?** yes -* **how do you communicate segment semantics to the user?** The type of the segment property which is stored inside Segmented Property Type Code Sequence is displayed to the user. -* **how do you support the user in defining the semantics of the object at the time segmentation is created?** The type of the segment \(i.e.Tumor, Implant, Bone and Undefined\) can be selected by the user when creating a Segmentation object. + * **are both single and multiple segments supported?** Current version of Brainlab SmartBrush can write only single-segment objects, but reads both single- and multi-segment + * **how are the overlapping segments handled?** The user can see the outline of the contour \(the area inside the the contour is slightly color-washed\) + * **do you support both BINARY and FRACTIONAL segmentation types?** Brainlab always exports segmentations as FRACTIONAL type and RLE-compressed + * **do you render the segment using the color specified in the DICOM object?** yes + * **how do you communicate segment semantics to the user?** The type of the segment property which is stored inside Segmented Property Type Code Sequence is displayed to the user. + * **how do you support the user in defining the semantics of the object at the time segmentation is created?** The type of the segment \(i.e.Tumor, Implant, Bone and Undefined\) can be selected by the user when creating a Segmentation object. -**Demonstration video on YouTube** \(recorded at RSNA 2015 DICOM4QI\): [https://youtu.be/2J3sxpqHtlY](https://youtu.be/2J3sxpqHtlY). + **Demonstration video on YouTube** \(recorded at RSNA 2015 DICOM4QI\): [https://youtu.be/2J3sxpqHtlY](https://youtu.be/2J3sxpqHtlY). -3.**Read task**: load each of the DICOM SEG datasets that accompany the imaging series into your platform + 3.**Read task**: load each of the DICOM SEG datasets that accompany the imaging series into your platform -**Test dataset \#1** + **Test dataset \#1** -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | + | Test dataset | Result of rendering | + | -- | -- | + | 3D Slicer | | -**Test dataset \#2** + **Test dataset \#2** -| Test dataset | Result of rendering | -| :--- | :--- | -| Brainlab | | + | Test dataset | Result of rendering | + | -- | -- | + | Brainlab | | -**Test dataset \#3** + **Test dataset \#3** -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | + | Test dataset | Result of rendering | + | -- | -- | + | 3D Slicer | | -**Test dataset \#4** + **Test dataset \#4** -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | + | Test dataset | Result of rendering | + | -- | -- | + | 3D Slicer | | -4.**Write task** + 4.**Write task** -`dciodvfy` checks produce no errors: + `dciodvfy` checks produce no errors: ```text (0x0069,0x1001) ? - Warning - Unrecognized tag - assuming explicit value representation OK @@ -56,8 +55,7 @@ Segmentation Warning - Unrecognized defined term <99BL-GEN> for value 1 of attribute ``` -| Output dataset | Result of rendering in Brainlab | -| :--- | :--- | -| [\#3 write result](http://slicer.kitware.com/midas3/download/item/266127/SEG_BL_DataSet3_compressed.dcm) | | -| [\#4 write result](http://slicer.kitware.com/midas3/download/item/266126/SEG_BL_DataSet4_compressed.dcm) | | - + | Output dataset | Result of rendering in Brainlab| + | -- | -- | + | [#3 write result](http://slicer.kitware.com/midas3/download/item/266127/SEG_BL_DataSet3_compressed.dcm) | | + | [#4 write result](http://slicer.kitware.com/midas3/download/item/266126/SEG_BL_DataSet4_compressed.dcm) | | diff --git a/content/results/seg/epad.md b/content/results/seg/epad.md index fe659f1..8307503 100644 --- a/content/results/seg/epad.md +++ b/content/results/seg/epad.md @@ -1,4 +1,3 @@ -# ePAD 1.**Description of the platform/product**: @@ -11,17 +10,15 @@ 2.**Description of the relevant features of the platform**: * **are both single and multiple segments supported?** the new viewer uses AMI and supports multisegments; whereas the old viewer supports only single segments. -* **how are the overlapping segments handled?** user can select either to view the outline or as filled \(see screenshot below showing both AIM on ClearCanvas and Slicer datasets from the Read task\) +* **how are the overlapping segments handled?** user can select either to view the outline or as filled \(see screenshot below showing both AIM on ClearCanvas and Slicer datasets from the Read task\) -![](../../.gitbook/assets/overlap_sc_stroke.png) +![](epad/overlap_sc_stroke.png) - \| - -![](../../.gitbook/assets/overlap_sc_fill.png) +![](epad/overlap_sc_fill.png) * **do you support both BINARY and FRACTIONAL segmentation types?** yes, segmentations that are saved as FRACTIONAL are mapped to gray scale \(see screenshot below showing a FRACTIONAL segmentation\) -![](../../.gitbook/assets/fractionalseg.png) +![](epad/fractionalseg.png) * **do you render the segment using the color specified in the DICOM object?** the new viewer uses AMI and renders using the color specified in the DICOM object; whereas the old viewer uses annotation owner's preferred color for all segmentations * **how do you communicate segment semantics to the user?** currently user has no means to get information about the semantics of the object as defined in the segmentation @@ -32,35 +29,21 @@ **Test dataset \#1** | Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | -| ePAD | | -| syngo.via | | -| AIMonClearCanvas | | -| Brainlab | | +| -- | -- | +| 3D Slicer | | +| ePAD | | +| syngo.via | | +| AIMonClearCanvas| | +| Brainlab| | **Test dataset \#2** -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | - -**Test dataset \#3** - -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | - -**Test dataset \#4** +At this time, ePAD does not support multi-segment segmentations. -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | 4.**Write task** * segment the lung lesion using any method available in your platform; save the result as DICOM SEG; please include in the series description the name of your tool to simplify comparison tasks! - * results are uploaded +* results are uploaded * run [dciodvfy DICOM validator](http://www.dclunie.com/dicom3tools/dciodvfy.html); iterate on resolving the identified issues as necessary - * no errors, only warnings from dciodvfy - +* no errors, only warnings from dciodvfy diff --git a/content/results/seg/index.md b/content/results/seg/index.md index 6f4552a..537909c 100644 --- a/content/results/seg/index.md +++ b/content/results/seg/index.md @@ -11,7 +11,6 @@ | [MITK](/results/seg/MITK.md) | | | | | [Mint Medical](/results/seg/mint.md) | | | | | XNAT | | | | -| Koelis | | | | | [Pixelmed DicomImageViewer](/results/seg/pixelmed.md) | | | | | [Siemens syngo.via](/results/seg/syngovia.md) ** * **| | | | | OsiriX Lite ** * **| | | | @@ -26,68 +25,3 @@ * - task completed * - no response received, or for some reason task could not be completed - -## 3D Slicer - -1.**Description of the platform/product**: - -* **name and version of the software**: 3D Slicer, Nightly release 4.7.0-2016-11-24, with Reporting extension installed -* **free?** yes [http://download.slicer.org](http://download.slicer.org) -* **commercial?** no -* **open source?** yes [http://github.com/slicer/slicer](http://github.com/slicer/slicer) -* **what DICOM library do you use?** [DCMTK](http://dcmtk.org), [DCMQI](http://github.com/qiicr/dcmqi) - -2.**Description of the relevant features of the platform**: - -* **are both single and multiple segments supported?** yes **how are the overlapping segments handled?** solid color of the outline is shown for all segments; inner area is shown semi-transparent \(see screenshot below showing both AIMonClearCanvas and Brainlab datasets from the Read task\) - - - - -* **do you support both BINARY and FRACTIONAL segmentation types?** only BINARY can be displayed; SEGs that are saved as FRACTIONAL will be read as BINARY \(i.e., no mapping to fractional occupancy or probability will be done\) -* **do you render the segment using the color specified in the DICOM object?** yes -* **how do you communicate segment semantics to the user?** Display of the segment semantics is provided in specialized Slicer modules. As of November 2016, semantics is shown in a tooltip over the color swatch in the list of segments in Segment Editor module \(see screenshot below\). Similar interface is provided in the Reporting module. - - -![](slicer/slicer-read-td3.png) - -* **how do you support the user in defining the semantics of the object at the time segmentation is created?** user can select from the terminology lists by double-clicking on the colored square while editing segment, see screenshot below. Color can also be specified. Certain combinations of codes have suggested colors. - -![](../../.gitbook/assets/terminology-selector.png) - -3.**Read task**: load each of the DICOM SEG datasets that accompany the imaging series into your platform - -**Test dataset \#1** - -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | -| syngo.via | | -| AIMonClearCanvas | | - -Note: Brainlab dataset could not be loaded, since it does not have SliceThickness attribute \(see CP-1426\). This issue has been since fixed in Brainlab, but test datasets 1 and 2 have not been updated. - -**Test dataset \#2** - -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | - -**Test dataset \#3** - -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | - -**Test dataset \#4** - -| Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | - -4.**Write task** - -* segment the lung lesion using any method available in your platform; save the result as DICOM SEG; please include in the series description the name of your tool to simplify comparison tasks! - * results are uploaded -* run [dciodvfy DICOM validator](http://www.dclunie.com/dicom3tools/dciodvfy.html); iterate on resolving the identified issues as necessary - * no errors, only warnings from dciodvfy diff --git a/content/results/seg/slicer.md b/content/results/seg/slicer.md index e32a3d8..a9b7307 100644 --- a/content/results/seg/slicer.md +++ b/content/results/seg/slicer.md @@ -1,5 +1,3 @@ -# 3D Slicer - 1.**Description of the platform/product**: * **name and version of the software**: 3D Slicer, Nightly release 4.7.0-2016-11-24, with Reporting extension installed @@ -12,47 +10,47 @@ * **are both single and multiple segments supported?** yes **how are the overlapping segments handled?** solid color of the outline is shown for all segments; inner area is shown semi-transparent \(see screenshot below showing both AIMonClearCanvas and Brainlab datasets from the Read task\) -![](../../.gitbook/assets/seg-overlap%20%281%29.png) + * **do you support both BINARY and FRACTIONAL segmentation types?** only BINARY can be displayed; SEGs that are saved as FRACTIONAL will be read as BINARY \(i.e., no mapping to fractional occupancy or probability will be done\) * **do you render the segment using the color specified in the DICOM object?** yes * **how do you communicate segment semantics to the user?** Display of the segment semantics is provided in specialized Slicer modules. As of November 2016, semantics is shown in a tooltip over the color swatch in the list of segments in Segment Editor module \(see screenshot below\). Similar interface is provided in the Reporting module. -![](../../.gitbook/assets/slicer-read-td3%20%281%29.png) +![](slicer/slicer-read-td3.png) * **how do you support the user in defining the semantics of the object at the time segmentation is created?** user can select from the terminology lists by double-clicking on the colored square while editing segment, see screenshot below. Color can also be specified. Certain combinations of codes have suggested colors. -![](../../.gitbook/assets/terminology-selector.png) + 3.**Read task**: load each of the DICOM SEG datasets that accompany the imaging series into your platform **Test dataset \#1** | Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | -| syngo.via | | -| AIMonClearCanvas | | +| -- | -- | +| 3D Slicer | | +| syngo.via | | +| AIMonClearCanvas| | Note: Brainlab dataset could not be loaded, since it does not have SliceThickness attribute \(see CP-1426\). This issue has been since fixed in Brainlab, but test datasets 1 and 2 have not been updated. **Test dataset \#2** | Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | +| -- | -- | +| 3D Slicer | | **Test dataset \#3** | Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | +| -- | -- | +| 3D Slicer | | **Test dataset \#4** | Test dataset | Result of rendering | -| :--- | :--- | -| 3D Slicer | | +| -- | -- | +| 3D Slicer | | 4.**Write task** @@ -60,4 +58,3 @@ Note: Brainlab dataset could not be loaded, since it does not have SliceThicknes * results are uploaded * run [dciodvfy DICOM validator](http://www.dclunie.com/dicom3tools/dciodvfy.html); iterate on resolving the identified issues as necessary * no errors, only warnings from dciodvfy - diff --git a/SUMMARY.md b/gitbook/SUMMARY.md similarity index 100% rename from SUMMARY.md rename to gitbook/SUMMARY.md diff --git a/book.json b/gitbook/book.json similarity index 100% rename from book.json rename to gitbook/book.json diff --git a/mkdocs.yml b/mkdocs.yml index d903fc8..0fedab5 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -23,9 +23,12 @@ pages: - Parametric maps: instructions/pm.md - Longitudinal annotation: instructions/longitudinal.md - Tractography (DICOM TR): instructions/tr.md - - Results: - - Organization: results/index.md - - Segmentation: results/seg/index.md + - Results organization: results/index.md + - Results - Segmentation: + - Summary: results/seg/index.md + - 3D Slicer: results/seg/slicer.md + - ePAD: results/seg/epad.md + - Brainlab: results/seg/brainlab.md - History: history.md - Referencs: refs.md