updates

QIICR · Nov 1, 2018 · ac976c7 · ac976c7
1 parent 6300453
commit ac976c7
Show file tree

Hide file tree

Showing 7 changed files with 69 additions and 154 deletions.
diff --git 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 | <img src="./brainlab/brainlab-read-lidc.png" width=250> |
 
-**Test dataset \#2**
+  **Test dataset \#2**
 
-| Test dataset | Result of rendering |
-| :--- | :--- |
-| Brainlab |   |
+  | Test dataset | Result of rendering |
+  | -- | -- |
+  | Brainlab | <img src="./brainlab/brainlab-read-seg2.png" width=250> |
 
-**Test dataset \#3**
+  **Test dataset \#3**
 
-| Test dataset | Result of rendering |
-| :--- | :--- |
-| 3D Slicer |     |
+  | Test dataset | Result of rendering |
+  | -- | -- |
+  | 3D Slicer | <img src="brainlab/brainlab-read-hnc.jpg" width=250> <img src="./brainlab/brainlab-read-hnc-measurements.jpg" width=250>|
 
-**Test dataset \#4**
+  **Test dataset \#4**
 
-| Test dataset | Result of rendering |
-| :--- | :--- |
-| 3D Slicer |   |
+  | Test dataset | Result of rendering |
+  | -- | -- |
+  | 3D Slicer | <img src="./brainlab/brainlab-read-prostate.jpg" width=250> |
 
-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 <Coding Scheme Designator>
 ```
 
-| 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) | <img src="brainlab/DataSet3_FromSmartbrush_ReadByBrainlabSmartbrush.JPG" width=250> <img src="brainlab/DataSet3_FromSmartbrush_ReadByBrainlabSmartbrush_UI.JPG" width=250> |
+  | [#4 write result](http://slicer.kitware.com/midas3/download/item/266126/SEG_BL_DataSet4_compressed.dcm) | <img src="brainlab/DataSet4_FromSmartbrush_ReadByBrainlabSmartbrush.JPG" width=250> <img src="brainlab/DataSet4_FromSmartbrush_ReadByBrainlabSmartbrush_UI.JPG" width=250>  |
diff --git 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 | <img src="epad/slicer_qin2.png" width=250> |
+| ePAD | <img src="epad/epad-read-lidc.png" width=250> |
+| syngo.via | <img src="epad/syngo_segmentations.png" width=250> |
+| AIMonClearCanvas| <img src="epad/clearcanvas_segmentation.png" width=250> |
+| Brainlab| <img src="epad/fractionalseg.png" width=250> |
 
 **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
@@ -11,7 +11,6 @@
 | [MITK](/results/seg/MITK.md) | <img src="../../images/done.png" width=25> | <img src="../../images/done.png" width=25> | <img src="../../images/done.png" width=25> |
 | [Mint Medical](/results/seg/mint.md) | <img src="../../images/done.png" width=25> | <img src="../../images/done.png" width=25> | <img src="../../images/done.png" width=25> |
 | XNAT | <img src="../../images/waiting.png" width=25> | <img src="../../images/waiting.png" width=25> | <img src="../../images/waiting.png" width=25> |
-| Koelis | <img src="../../images/failed.png" width=25> | <img src="../../images/failed.png" width=25> | <img src="../../images/failed.png" width=25> |
 | [Pixelmed DicomImageViewer](/results/seg/pixelmed.md) | <img src="../../images/done.png" width=25> | <img src="../../images/done.png" width=25> | <img src="../../images/failed.png" width=25> |
 | [Siemens syngo.via](/results/seg/syngovia.md) ** * **| <img src="../../images/done.png" width=25> | <img src="../../images/failed.png" width=25> | <img src="../../images/done.png" width=25> |
 | OsiriX Lite ** * **| <img src="../../images/done.png" width=25> | <img src="../../images/failed.png" width=25> | <img src="../../images/failed.png" width=25> |
@@ -26,68 +25,3 @@
 * <img src="../../images/done.png" width=25> - task completed
 
 * <img src="../../images/failed.png" width=25> - 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 \(see screenshot below showing both AIMonClearCanvas and Brainlab datasets from the Read task\)
-
-<img src="slicer/seg-overlap.png" width="50%"">
-
-
-* **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.
-
-<img src="slicer/slicer-read-td3.png" width="50%"">
-![](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
@@ -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
@@ -12,52 +10,51 @@
 
 * **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)
+<img src="slicer/seg-overlap.png" width="50%"">
 
 * **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)
+<img src="slicer/terminology-selector.png" width="50%">
 
 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 | <img src="slicer/slicer-read-lidc.png" width="50%"> |
+| syngo.via | <img src="slicer/syngo-read-lidc.png" width="50%"> |
+| AIMonClearCanvas| <img src="slicer/aimclearcanvas-read-lidc.png" width="50%"> |
 
 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 | <img src="./slicer/slicer-read-td2.png"> |
 
 **Test dataset \#3**
 
 | Test dataset | Result of rendering |
-| :--- | :--- |
-| 3D Slicer |   |
+| -- | -- |
+| 3D Slicer | <img src="./slicer/slicer-read-td3.png" width="50%"> |
 
 **Test dataset \#4**
 
 | Test dataset | Result of rendering |
-| :--- | :--- |
-| 3D Slicer |   |
+| -- | -- |
+| 3D Slicer | <img src="./slicer/slicer-read-td4.png" width="50%"> |
 
 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/SUMMARY.md → gitbook/SUMMARY.md b/SUMMARY.md → gitbook/SUMMARY.md
diff --git a/book.json → gitbook/book.json b/book.json → gitbook/book.json
diff --git 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