https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=AmasNAMIC Wiki - User contributions [en]2026-05-17T15:51:52ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/Needle_Segmentation_from_MRI&diff=947952017 Winter Project Week/Needle Segmentation from MRI2017-01-11T12:09:20Z<p>Amas: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Ziyang Wang, BWH<br />
* Alireza Mehrtash, BWH<br />
* Alireza Ziaei Torbati, BWH<br />
* Guillaume Pernelle, Imperial College London<br />
* Paolo Zaffino, Magna Graecia University of Catanzaro, Italy<br />
* Andre Mastmeyer, University of Luebeck, Germany<br />
* Tina Kapur, BWH/HMS<br />
<br />
==Project Description==<br />
<br />
This project is a continuation of the project started during the 2016 summer project week ([[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]]), [http://needlefinder.org NeedleFinder] offers tools to segment needles from MRI/CT. It has mostly been tested on MRI from GYN brachytherapy cases. Currently the user must provide the needle tip for the segmentation to start. We aim to detect the tip automatically to make the needle segmentation fully automatic.<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Automatic detection of needle tips in MRI from GYN brachytherapy cases.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* We have manually segmented around 1k needles from GYN brachytherapy cases. We want to use this data in a supervised learning approach.<br />
* We have a pipeline for preprocessing the data (image spacing and normalization)<br />
* TODO: choose between 2 strategies: <br />
** Continue with the binary classification approach -> in the region of interest, voxels are classified as positive (needle) or negative (background). Challenge: link those voxels together to form needles / filter out false negatives. Alternative: try to find the tip position and use the previous algorithm to segment the needle<br />
** Use a semantic segmentation approach (fully convolutional neural networks [J Long 2015], Region-based semantic segmentation with end-to-end training [Caesar 2016])<br />
<br />
...<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
<br />
</div><br />
</div></div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88546NeedleFinder2015-01-09T05:29:48Z<p>Amas: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 5/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - idea abandoned<br />
** Wednesday started - Thursday finished<br />
** Thursday started - Friday morning finished<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a new temporary fiducial marker for easier manual needle tracking using the sagittal and axial views. We standardized the workflow by guiding the user though the steps (e.g. providing the axial limit slice is now mandatory as a first step). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons in the left panel. The last inserted needle can be deleted (with CTRL+Z or button) and the module can be easily reset. The layout of the module UI has been cleaned up.<br />
<br />
- Code profiling : We went through the code to clarify many open questions, removed unused functions. We built a table summarizing the global purpose of each function (function tagging). We developed a profiling method using print commands and message boxes (using the inspect library).<br />
<br />
- Bounding box approach : We discussed this proposal, and found, after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user than defining a complete bounding box. Needle tip clicks are given in this axial view after tracking the needle canals upwards in the sagittal view. So, the idea is not furtherly addressed here.<br />
<br />
- Tip detection : We wrote a script using SimpleITK to extract and re-sample all the tip regions from images using needles from manual segmentation. These 115 cubical regions can now be used for data analysis (machine learning). As a first step, we built an average model (template) of the needle tips to be matched to new data sets, e.g. using convolution/correlation filters:<br />
<pictures of 3 needle tips with artifacts><br />
<picture of the average tip model><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurately. For now, the origin is registered, but the orientation could be improved. After convolution (SimpleITK) the average needle tip model with a patient MR image, this approach suffers from over-segmentation.<br />
<br />
- NeedleFinder parameter optimization : We use the workshop as a kickoff on this topic and want to compare the performance of a brute force/randomized parameter search approach with a genetic algorithm after the workshop. Therefore the implementation of a genetic algorithm has been completed (to be able to find a global optimum faster). A cost/fitness function was designed for our problem. Because the parameter optimization is still computationally expensive (several needle detections carried out in every iteration), only exemplary results for individual patients, but not a patient collective could be obtained here.<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88545NeedleFinder2015-01-09T05:23:15Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 5/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - idea abandoned<br />
** Wednesday started - Thursday finished<br />
** Thursday started - Friday morning finished<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a new temporary fiducial marker for easier manual needle tracking using the sagittal and axial views. We standardized the workflow by guiding the user though the steps (e.g. providing the axial limit slice is now mandatory as a first step). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons in the left panel. The last inserted needle can be deleted (with CTRL+Z or button) and the module can be easily reset. The layout of the module UI has been cleaned up.<br />
<br />
- Code profiling : We went through the code to clarify many open questions, removed unused functions. We built a table summarizing the global purpose of each functions (function tagging). We developed a profiling method using print commands and message boxes (using the inspect library).<br />
<br />
- Bounding box approach : We discussed this proposal, and found, after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user than defining a complete bounding box. Needle tip clicks are given in this axial view after tracking the needle canals upwards in the sagittal view. So, the idea is not furtherly addressed here.<br />
<br />
- Tip detection : We wrote a script using SimpleITK to extract and re-sample all the tip regions from images using needles from manual segmentation. These 115 cubical regions can now be used for data analysis (machine learning). As a first step, we built an average model (template) of the needle tips to be matched to new data sets, e.g. using convolution/correlation filters:<br />
<pictures of 3 needle tips with artifacts><br />
<picture of the average tip model><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurately. For now, the origin is registered, but the orientation could be improved. After convolution (SimpleITK) the average needle tip model with a patient MR image, this approach suffers from over-segmentation.<br />
<br />
- NeedleFinder parameter optimization : We use the workshop as a kickoff on this topic and want to compare the performance of a brute force/randomized parameter search approach with a genetic algorithm after the workshop. Therefore the implementation of a genetic algorithm has been completed (to be able to find a global optimum faster). A cost/fitness function was designed for our problem. Because the parameter optimization is still computationally expensive (several needle detections carried out in every iteration), only exemplary results for individual patients, but not a patient collective could be obtained here.<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88544NeedleFinder2015-01-09T05:21:05Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 5/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started - Friday morning finished<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a new temporary fiducial marker for easier manual needle tracking using the sagittal and axial views. We standardized the workflow by guiding the user though the steps (e.g. providing the axial limit slice is now mandatory as a first step). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons in the left panel. The last inserted needle can be deleted (with CTRL+Z or button) and the module can be easily reset. The layout of the module UI has been cleaned up.<br />
<br />
- Code profiling : We went through the code to clarify many open questions, removed unused functions. We built a table summarizing the global purpose of each functions (function tagging). We developed a profiling method using print commands and message boxes (using the inspect library).<br />
<br />
- Bounding box approach : We discussed this proposal, and found, after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user than defining a complete bounding box. Needle tip clicks are given in this axial view after tracking the needle canals upwards in the sagittal view. So, the idea is not furtherly addressed here.<br />
<br />
- Tip detection : We wrote a script using SimpleITK to extract and re-sample all the tip regions from images using needles from manual segmentation. These 115 cubical regions can now be used for data analysis (machine learning). As a first step, we built an average model (template) of the needle tips to be matched to new data sets, e.g. using convolution/correlation filters:<br />
<pictures of 3 needle tips with artifacts><br />
<picture of the average tip model><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurately. For now, the origin is registered, but the orientation could be improved. After convolution (SimpleITK) the average needle tip model with a patient MR image, this approach suffers from over-segmentation.<br />
<br />
- NeedleFinder parameter optimization : We use the workshop as a kickoff on this topic and want to compare the performance of a brute force/randomized parameter search approach with a genetic algorithm after the workshop. Therefore the implementation of a genetic algorithm has been completed (to be able to find a global optimum faster). A cost/fitness function was designed for our problem. Because the parameter optimization is still computationally expensive (several needle detections carried out in every iteration), only exemplary results for individual patients, but not a patient collective could be obtained here.<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88542NeedleFinder2015-01-09T05:19:27Z<p>Amas: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 4/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a new temporary fiducial marker for easier manual needle tracking using the sagittal and axial views. We standardized the workflow by guiding the user though the steps (e.g. providing the axial limit slice is now mandatory as a first step). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons in the left panel. The last inserted needle can be deleted (with CTRL+Z or button) and the module can be easily reset. The layout of the module UI has been cleaned up.<br />
<br />
- Code profiling : We went through the code to clarify many open questions, removed unused functions. We built a table summarizing the global purpose of each functions (function tagging). We developed a profiling method using print commands and message boxes (using the inspect library).<br />
<br />
- Bounding box approach : We discussed this proposal, and found, after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user than defining a complete bounding box. Needle tip clicks are given in this axial view after tracking the needle canals upwards in the sagittal view. So, the idea is not furtherly addressed here.<br />
<br />
- Tip detection : We wrote a script using SimpleITK to extract and re-sample all the tip regions from images using needles from manual segmentation. These 115 cubical regions can now be used for data analysis (machine learning). As a first step, we built an average model (template) of the needle tips to be matched to new data sets, e.g. using convolution/correlation filters:<br />
<pictures of 3 needle tips with artifacts><br />
<picture of the average tip model><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurately. For now, the origin is registered, but the orientation could be improved. After convolution (SimpleITK) the average needle tip model with a patient MR image, this approach suffers from over-segmentation.<br />
<br />
- NeedleFinder parameter optimization : We use the workshop as a kickoff on this topic and want to compare the performance of a brute force/randomized parameter search approach with a genetic algorithm after the workshop. Therefore the implementation of a genetic algorithm has been completed (to be able to find a global optimum faster). A cost/fitness function was designed for our problem. Because the parameter optimization is still computationally expensive (several needle detections carried out in every iteration), only exemplary results for individual patients, but not a patient collective could be obtained here.<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88541NeedleFinder2015-01-09T05:16:27Z<p>Amas: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 4/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a new temporary fiducial marker for easier manual needle tracking. We standardized the workflow by guiding the user though the steps (e.g. providing the axial limit slice is now mandatory as a first step). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons in the left panel. The last inserted needle can be deleted (with CTRL+Z or button) and the module can be easily reset. The layout of the module UI has been cleaned up.<br />
<br />
- Code profiling : We went through the code to clarify many open questions, removed unused functions. We built a table summarizing the global purpose of each functions (function tagging). We developed a profiling method using print commands and message boxes (using the inspect library).<br />
<br />
- Bounding box approach : We discussed this proposal, and found, after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user than defining a complete bounding box.<br />
<br />
- Tip detection : We wrote a script using SimpleITK to extract and re-sample all the tip regions from images using needles from manual segmentation. These 115 cubical regions can now be used for data analysis (machine learning). As a first step, we built an average model (template) of the needle tips to be matched to new data sets, e.g. using convolution/correlation filters:<br />
<pictures of 3 needle tips with artifacts><br />
<picture of the average tip model><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurately. For now, the origin is registered, but the orientation could be improved. After convolution (SimpleITK) the average needle tip model with a patient MR image, our approach suffers from oversegmentation.<br />
<br />
- NeedleFinder parameter optimization : We use the workshop as a kickoff on this topic and want to compare the performance of a brute force/randomized parameter search approach with a genetic algorithm after the workshop. Therefore the implementation of a genetic algorithm has been completed (to be able to find a global optimum faster). A cost/fitness function was designed for our problem. Because the parameter optimization is still computationally expensive (several needle detections carried out in every iteration), only exemplary results for individual patients, but not a patient collective could be obtained here.<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88536NeedleFinder2015-01-09T03:47:02Z<p>Amas: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 4/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a temporary fiducial marker for easier manual needle tracking. We standardized the workflow by guiding the user though the steps (eg. providing the axial limit slice is now mandatory). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons. The last inserted needle can be deleted (with CTRL+Z or button) and the scene can be easily reset. Layout of the module UI has been cleaned up.<br />
The results can be viewed in the NeedleFinder tutorial project: [http://www.na-mic.org/Wiki/index.php/Needle_Finder_Tutorial]. <br />
<br />
- Code profiling : We went through the code to clarify opened questions, removed unused functions. We built a table summarizing the global purpose of each functions (function tagging). We developed a profiling method using message boxes (using the inspect library).<br />
<br />
- Bounding box approach: we discussed this proposal, and found, after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user than defining a complete bounding box.<br />
<br />
- Tip detection : We wrote a script to extract, transform and re-sample all the tips from images with needles from manual segmentation. These 115 cubical regions can now be used for data analysis, machine learning. We built an average model of the needle tips to be matched to new data sets, e.g. using convolution filters:<br />
<pictures of 3 needle tips with artifacts><br />
<picture of the model><br />
<picture of the results of the convolution filter><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurate. For now, the origin is registered, but the orientation could be improved. After convolution the average needle tip model with a patient MR image, our approach suffers from oversegmentation.<br />
<br />
- NeedleFinder parameter optimization : we want to use the workshop as a kickoff on this topic and want to compare the performance of a brute force/randomized parameter search approach with a genetic algorithm after the workshop. Therefore the implementation of a genetic algorithm was carried out (to find an optimum faster). A cost function was designed for our problem. Because the parameter optimization is still computationally expensive, only exemplary results for individual patients, but not a patient collective could be obtained here.<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88535NeedleFinder2015-01-09T03:35:00Z<p>Amas: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 4/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a temporary fiducial marker for easier manual needle tracking. We standardized the workflow by guiding the user though the steps (eg. providing the axial limit slice is now mandatory). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons. The last inserted needle can be deleted (with CTRL+Z or button) and the scene can be easily reset. Layout of the module UI has been cleaned up.<br />
The results can be viewed in the NeedleFinder tutorial project: [http://www.na-mic.org/Wiki/index.php/Needle_Finder_Tutorial]. <br />
<br />
- Code profiling : We went through the code to clarify opened questions, removed unused functions. We built a table summarising the global purpose of each functions (function taging). We developed a profiling method using message boxes (using the inspect library).<br />
<br />
- Bounding box approach: we discussed this proposal, and found after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user.<br />
<br />
- Tip detection : We wrote a script to extract, transform and resample all the tips from images with needles from manual segmentation. These 115 cubical regions can now be used for data analysis, machine learning. We built an average model of the needle tips to be matched to new datasets eg. using convolution filters:<br />
<pcitures of 3 needle tips with artifacts><br />
<picture of the model><br />
<picture of the results of the convolution filter><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurate. For now, the origin is registered, but the orientation could be improved. After convoluting the average needle tip model with a patient MR image, our simple approach suffers from oversegmentation.<br />
<br />
- Parameter optimization: we want to compare the performance of a brute force/randomized parameter search approach with a genetic algorithm after the workshop. Therefore this implementation of a genetic algorithm was carried out (to find an optimum faster). A cost function was designed for our problem. Because the parameter optimization is still computationally expensive only exemplary results for individual patients, but not a patient collective could be obtained.<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=Needle_Finder_Tutorial&diff=88474Needle Finder Tutorial2015-01-08T22:30:32Z<p>Amas: /* Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Gao Yang, <br />
Andre Mastmeyer, <br />
Guillaume Pernelle, <br />
Tina Kapur<br />
<br />
==Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
This tutorial gives an example of using Slicer4 for Needle Finder.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Plan</h3><br />
Topics covered include:<br />
*Data Loading<br />
*Choose Module<br />
*Segmentation<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"></div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88473NeedleFinder2015-01-08T22:26:47Z<p>Amas: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 4/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a temporary fiducial marker for easier manual needle tracking. We standardized the workflow by guiding the user though the steps (eg. providing the axial limit slice is now mandatory). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons. The last inserted needle can be deleted (with CTRL+Z or button) and the scene can be easily reset. Layout of the module UI has been cleaned up.<br />
The results can be viewed in the NeedleFinder tutorial project: [http://www.na-mic.org/Wiki/index.php/Needle_Finder_Tutorial]. <br />
<br />
- Code profiling : We went through the code to clarify opened questions, removed unused functions. We built a table summarising the global purpose of each functions (function taging). We developed a profiling method using message boxes (using the inspect library).<br />
<br />
- Bounding box approach: we discussed this proposal, and found after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user.<br />
<br />
- Tip detection : We wrote a script to extract, transform and resample all the tips from images with needles from manual segmentation. These 115 cubical regions can now be used for data analysis, machine learning. We built an average model of the needle tips to be matched to new datasets eg. using convolution filters:<br />
<pcitures of 3 needle tips with artifacts><br />
<picture of the model><br />
<picture of the results of the convolution filter><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurate. For now, the origin is registered, but the orientation could be improved. After convoluting the average needle tip model with a patient MR image, our simple approach suffers from oversegmentation.<br />
<br />
- Parameter optimization: now!<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88472NeedleFinder2015-01-08T22:26:00Z<p>Amas: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 4/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a temporary fiducial marker for easier manual needle tracking. We standardized the workflow by guiding the user though the steps (eg. providing the axial limit slice is now mandatory). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons. The last inserted needle can be deleted (with CTRL+Z or button) and the scene can be easily reset. Layout of the module UI has been cleaned up.<br />
The results can be viewed in the NeedleFinder tutorial project: [http://www.na-mic.org/Wiki/index.php/Needle_Finder_Tutorial]. <br />
<br />
- Code profiling : We went through the code to clarify opened questions, removed unused functions. We built a table summarising the global purpose of each functions (function taging). We developed a profiling method using message boxes (using the inspect library).<br />
<br />
- Tip detection : We wrote a script to extract, transform and resample all the tips from images with needles from manual segmentation. These 115 cubical regions can now be used for data analysis, machine learning. We built an average model of the needle tips to be matched to new datasets eg. using convolution filters:<br />
<pcitures of 3 needle tips with artifacts><br />
<picture of the model><br />
<picture of the results of the convolution filter><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurate. For now, the origin is registered, but the orientation could be improved. After convoluting the average needle tip model with a patient MR image, our simple approach suffers from oversegmentation.<br />
<br />
- Bounding box approach: we discussed this proposal, and found after slicing to the obturator base, just zooming into the image in the axial view is much easier for the user.<br />
<br />
- Parameter optimization: now!<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88471NeedleFinder2015-01-08T22:24:19Z<p>Amas: /* Project Results */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 4/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==Project Results==<br />
<br />
- GUI and workflow : We improved the workflow and the GUI of the slicer module NeedleFinder: the needle grouping feature has been removed, we introduced a temporary fiducial marker for easier manual needle tracking. We standardized the workflow by guiding the user though the steps (eg. providing the axial limit slice is now mandatory). We introduced new keyboard shortcuts, thus the user can stay focused on the segments, not changing his mouse position to click buttons. The last inserted needle can be deleted (with CTRL+Z or button) and the scene can be easily reset. Layout of the module UI has been cleaned up.<br />
The results can be viewed in the NeedleFinder tutorial project: [http://www.na-mic.org/Wiki/index.php/Needle_Finder_Tutorial]. <br />
<br />
- Code profiling : We went through the code to clarify opened questions, removed unused functions. We built a table summarising the global purpose of each functions (function taging). We developed a profiling method using message boxes (using the inspect library).<br />
<br />
- Tip detection : We wrote a script to extract, transform and resample all the tips from images with needles from manual segmentation. These 115 cubical regions can now be used for data analysis, machine learning. We built an average model of the needle tips to be matched to new datasets eg. using convolution filters:<br />
<pcitures of 3 needle tips with artifacts><br />
<picture of the model><br />
<picture of the results of the convolution filter><br />
Our hypothesis that the needle tip artifact show out in the average needle tip model could not be confirmed at this time: We need to use more cases with needle tip artifacts (instead of mixing with other cases from other MR sequences). Secondly, we should sort out the needle tips from the obturator needles. Third, the little cubic image around the needle tip could be registered to each other before averaging to fit more accurate. For now, the origin is registered, but the orientation could be improved. After convoluting the average needle tip model with a patient MR image, our simple approach suffers from oversegmentation.<br />
<br />
- Parameter optimization: now!<br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88467NeedleFinder2015-01-08T21:53:01Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 4/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88466NeedleFinder2015-01-08T21:52:26Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 3/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started - Thursday finished<br />
** Thursday started<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88449NeedleFinder2015-01-08T14:21:18Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (build mean model from small ROIs around manually segmented needle tips)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 3/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started<br />
** Thursday<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88434NeedleFinder2015-01-07T21:49:30Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: 3/5<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started<br />
** Thursday<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88433NeedleFinder2015-01-07T21:48:17Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** Tuesday started - Wednesday finished<br />
** Tuesday started - Wednesday finished<br />
*** Tuesday started / Wednesday - to discuss later<br />
** Wednesday started<br />
** Thursday<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88389NeedleFinder2015-01-06T16:12:56Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** Tuesday started<br />
** Tuesday started<br />
*** Tuesday started / Wednesday<br />
** Wednesday<br />
** Thursday<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88032NeedleFinder2014-12-19T21:36:28Z<p>Amas: /* References */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88030NeedleFinder2014-12-19T20:58:07Z<p>Amas: /* References */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle Finder 2013 User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88029NeedleFinder2014-12-19T20:57:42Z<p>Amas: /* References */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle 2013 Finder User Guide]<br />
* [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88028NeedleFinder2014-12-19T20:57:28Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder, see [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle 2013 Finder User Guide]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88026NeedleFinder2014-12-19T20:55:55Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI and interaction simplification<br />
*** Provide Bounding Box/Region of Interest for better visualization and constrain search space for algorithms<br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle 2013 Finder User Guide]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88023NeedleFinder2014-12-19T20:49:33Z<p>Amas: /* References */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]<br />
* [https://docs.google.com/document/d/1Xvi6BYiiSiNlqoVQgRTWy6KiB7CqUEmH2EWFt4cuBQc/edit?usp=sharing Needle 2013 Finder User Guide]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88016NeedleFinder2014-12-19T20:14:47Z<p>Amas: /* References */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/NeedleFinder Needle Finder extension documentation]</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88015NeedleFinder2014-12-19T18:51:39Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Needle Finder 2013 Video]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
*ADD LINK FOR EXISTING DOCUMENTATION FOR NEEDLE FINDER IN SLICER, Andre-Tina: FROM YANG?</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88014NeedleFinder2014-12-19T18:50:01Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder * [https://www.wuala.com/mastmeyer/Share/AMIGO/NeedleFinder2013.mp4/?key=pxJNGGE3bTRh Demo Video]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
*ADD LINK FOR EXISTING DOCUMENTATION FOR NEEDLE FINDER IN SLICER, Andre-Tina: FROM YANG?</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88013NeedleFinder2014-12-19T17:22:42Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder * [https://www.wuala.com/mastmeyer/Share/AMIGO/Test.mpeg/?key=pxJNGGE3bTRh Demo Video]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
*ADD LINK FOR EXISTING DOCUMENTATION FOR NEEDLE FINDER IN SLICER, Andre-Tina: FROM YANG?</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88012NeedleFinder2014-12-19T17:21:36Z<p>Amas: /* References */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder [ADD A SHORT MOVIE TO SHOW WHAT IT DOES TODAY]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
*ADD LINK FOR EXISTING DOCUMENTATION FOR NEEDLE FINDER IN SLICER, Andre-Tina: FROM YANG?</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88011NeedleFinder2014-12-19T17:01:46Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder [ADD A SHORT MOVIE TO SHOW WHAT IT DOES TODAY]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Overall: N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
*ADD LINK FOR EXISTING DOCUMENTATION FOR NEEDLE FINDER IN SLICER</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88010NeedleFinder2014-12-19T17:00:42Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder [ADD A SHORT MOVIE TO SHOW WHAT IT DOES TODAY]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* N/Y<br />
** N/Y<br />
** N/Y<br />
*** N/Y<br />
** N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
*ADD LINK FOR EXISTING DOCUMENTATION FOR NEEDLE FINDER IN SLICER</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=88009NeedleFinder2014-12-19T17:00:04Z<p>Amas: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Yang Gao,<br />
Tina Kapur,<br />
Steve Pieper,<br />
Ron Kikinis<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Improve performance and usability of NeedleFinder [ADD A SHORT MOVIE TO SHOW WHAT IT DOES TODAY]<br />
** Code profiling, refactoring<br />
** GUI simplification<br />
*** Provide Bounding Box/Region of Interest <br />
** Semi-Automatic needle tip (and body) detection <br />
** Parameter optimization<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Improvements of the source code quality, algorithms and GUI (usability):<br />
** Ad-hoc python profiling concept (method tagging, logging and message boxes as code probes)<br />
** Improved standardized and guided workflow more usable by MDs (state machine)<br />
*** Interaction protocol using existing tools for MD to provide bounding-box quickly<br />
** Incorporate SimpleITK filtering/preprocessing and a little user interaction (try e.g. derivatives: gradient magnitude, vesselness)<br />
** Look into machine learning (implement simple genetic algorithm & compare to brute-force grid search)<br />
<!-- ** Rigid registration of CAD models to (preprocessed) scene (ICP, Besl) --><br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
</div><br />
</div><br />
<br />
==References==<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/24505784 Validation of catheter segmentation for MR-guided gynecologic cancer brachytherapy. Med Image Comput Comput Assist Interv. 2013;16(Pt 3):380-7.]<br />
*ADD LINK FOR EXISTING DOCUMENTATION FOR NEEDLE FINDER IN SLICER</div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=87942NeedleFinder2014-12-16T20:30:41Z<p>Amas: </p>
<hr />
<div>Here we will fill in tomorrow...<br />
<br />
__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Tina Kapur<br />
<br />
==Project Description (Draft by Andre)==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Automatic needle tip detection<br />
* Modelfit of oburator base and tube using CAD models<br />
* NF detection parameter optimization<br />
* Code profiling (is the code used?), refactoring<br />
* GUI improvements<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* SimpleITK filtering (e.g. derivatives: gradient magnitude, vesselness etc.)<br />
* Rigid registration of CAD models to (preprocessed) scene (ICP, Besl)<br />
* Machine learning (genetic algorithm etc.)<br />
* New ad-hoc python profiling concept (logging and message boxes as code probes)<br />
* Improved standardized and guided workflow more usable by MDs (disabling unsuitable buttons)<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
</div><br />
</div></div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=87941NeedleFinder2014-12-16T18:52:40Z<p>Amas: </p>
<hr />
<div>Here we will fill in tomorrow...<br />
<br />
__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
Andre Mastmeyer,<br />
Guillaume Pernelle,<br />
Tina Kapur<br />
<br />
==Project Description (Draft by Andre)==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Automatic needle tip detection<br />
* Modelfit of oburator base and tube using CAD models<br />
* NF detection parameter optimization<br />
* Code profiling (is the code used?), refactoring<br />
* GUI improvements<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* SimpleITK filtering (e.g. derivatives: gradient magnitude, vesselness etc.)<br />
* Rigid registration of CAD models to (preprocessed) scene (ICP, Besl)<br />
* Machine learning machine learning (genetic algorithm etc.)<br />
* New ad-hoc python profiling concept (logging and message boxes as code probes)<br />
* Improved standardized workflow more usable by MDs<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
* N/Y<br />
</div><br />
</div></div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=87940NeedleFinder2014-12-15T23:40:26Z<p>Amas: </p>
<hr />
<div>Here we will fill in tomorrow...<br />
<br />
__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
*<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Amashttps://www.na-mic.org/w/index.php?title=NeedleFinder&diff=87939NeedleFinder2014-12-15T23:39:31Z<p>Amas: Created page with 'Here we will fill in tomorrow...'</p>
<hr />
<div>Here we will fill in tomorrow...</div>Amashttps://www.na-mic.org/w/index.php?title=2015_Winter_Project_Week&diff=879382015 Winter Project Week2014-12-15T23:39:11Z<p>Amas: /* Projects */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-2015SLC.png|300px]]<br />
<br />
Welcome to the 20th Project week page! <br />
<br />
<br />
<br />
== Introduction ==<br />
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week. <br />
<br />
[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. <br />
<br />
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.<br />
<br />
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.<br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past|here]].<br />
<br />
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.<br />
<br />
Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
<br />
== '''Logistics''' ==<br />
*'''Dates:''' January 5-9, 2015.<br />
*'''Location:''' Salt Lake City, Utah<br />
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.<br />
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.<br />
<br />
== Agenda== <br />
{| border="1" cellpadding="5"<br />
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center" <br />
| style="width:5%"| '''Time'''<br />
| style="width:19%" | '''Monday, January 5''' <br />
| style="width:19%" | '''Tuesday, January 6'''<br />
| style="width:19%" | '''Wednesday, January 7''' <br />
| style="width:19%" | '''Thursday, January 8'''<br />
| style="width:19%" | '''Friday, January 9''' <br />
|-<br />
| style="background:#eeeeee; color:black"|<br />
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font><br />
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font><br />
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font><br />
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font><br />
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font><br />
|-<br />
| style="background:#eeeeee; color:black"|'''7:30-8:00''' <br />
| style="background:#ffffff; color:black"| <br />
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font><br />
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font><br />
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font><br />
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font><br />
|-<br />
| style="background:#eeeeee; color:black"|'''8:00-10:00''' <br />
| <br><font color="#9966cc"></font><br />
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br> <br />
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br> <br />
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font><br />
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font><br />
|-<br />
| style="background:#eeeeee; color:black"|'''10:00-10:30'''<br />
| style="background:#ffffff; color:black"|<br />
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''<br />
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''<br />
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''<br />
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''<br />
|-<br />
| style="background:#eeeeee; color:black"|'''10:30-12:00'''<br />
| <br />
| <br />
| <br />
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font><br />
|<br />
|-<br />
| style="background:#eeeeee; color:black"|'''12:00-1:00''' <br />
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br />
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br> <br />
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br> <br />
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br />
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font> <br />
|-<br />
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l <br />
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font><br />
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]] <br />
| <font color="#44AA88">''(Olympus B)''</font><br />
|<br />
|<br />
|-<br />
| style="background:#eeeeee; color:black"|'''3:00-3:30''' <br />
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''<br />
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''<br />
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''<br />
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''<br />
| style="background:#ffffff; color:black"|<br />
|-<br />
| style="background:#eeeeee; color:black"|'''3:00-5:00''' <br />
|<br />
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 2)'' <br> <!--[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>--><br />
| style="background:#ffffff; color:black"|<br />
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font><br />
| style="background:#ffffff; color:black"|<br />
|-<br />
| style="background:#eeeeee; color:black"|'''05:00-07:00''' <br />
| style="background:#dbf3ff; color:black"|<br />
| style="background:#dbf3ff; color:black"|<br />
| style="background:#dbf3ff; color:black"|<br />
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)<br />
| style="background:#ffffff; color:black"| <br />
|}<br />
<br />
=Projects=<br />
* [[2015_Project_Week_Template | Template for project pages]]<br />
* [[NeedleFinder | Image-based Needle Detection from MRI]]<br />
<br />
==Image-Guided Therapy==<br />
*Image-based Needle Detection from MRI; bridging Slicer and MeVis Lab (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)<br />
*Tracked ultrasound benchtop experment system for neurosurgery (Steve Pieper, Jim Miller)<br />
*Case review for interactive registration (Steve Pieper, Jim Miller, Alireza Mehrtash)<br />
*Workflow for percutaneous needle place (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)<br />
*Registration of pre-op and intra-op DTI to correlate paramets with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)<br />
*Prostate segmentation and biopsy (Peter Behringer, Andrey Fedorov)<br />
*Needle Detection Tutorial (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)<br />
<br />
==Huntington's Disease==<br />
<br />
==TBI==<br />
<br />
==Stroke==<br />
<br />
==Cardiac==<br />
<br />
== Lung ==<br />
<br />
*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Raul San Jose, Jim Miller)<br />
<br />
==Head and Neck Cancer / Radiotherapy ==<br />
<br />
==[http://qiicr.org QIICR]==<br />
* Mechanism to pull related DICOM series on derived modality load (Andrey, Csaba)<br />
* Segmentation object and enhanced multiframe object IO in DCMTK and Slicer (Steve, Andrey, Michael)<br />
*T1 mapping for variable flip angle (Artem, Xiao, Andrey)<br />
<br />
==Feature Extraction==<br />
<br />
==Additional Brain Image Analysis==<br />
<br />
==Slicer4 Extensions==<br />
* PET Tumor Segmentation (Christian Bauer)<br />
<br />
<br />
==TMJOA RO1 - Collaboration with NAMIC==<br />
* Improved model display (Francois Boudin, Steve Pieper)<br />
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==Infrastructure==<br />
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* Micro and Macro Scale in Slicer (Nicole Aucoin, Bradley Lowekamp)<br />
* Rulers in Markups module (Nicole Aucoin)<br />
<br />
== '''Registrants''' ==<br />
<br />
Do not add your name to this list - it is maintained by the organizers based on your paid registration. <br />
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<br />
# Aucoin , Nicole ; Brigham and Womens Hospital<br />
# Azizi Koutenaei , Bamshad ; Childrens National Health System<br />
# Bauer , Christian ; University of Iowa<br />
# Behringer , Peter ; Brigham and Womens Hospital<br />
# Budin , Francois ; UNC<br />
# Da , Xiao ; Athinoula A. Martinos Center for Biomedical Imaging<br />
# Fedorov , Andriy ; Brigham and Womens Hospital<br />
# Gonzalez , German ; Brigham and Womens Hospital<br />
# Harmouche , Rola ; Brigham and Womens Hospital<br />
# Johnson , Hans ; University of Iowa<br />
# Kapur , Tina ; Brigham and Womens Hospital<br />
# Kikinis , Ron ; Brigham and Womens Hospital<br />
# Kim , Eun Young Regina ; University of Iowa<br />
# Li , Ming ; BWH<br />
# MASTMEYER , Andre ; Brigham and Womens Hospital<br />
# Mehrtash , Alireza ; Brigham and Womens Hospital<br />
# Miller , James ; GE Global Research<br />
# Onieva Onieva , Jorge ; Brigham and Womens Hospital<br />
# Pieper , Steve ; Isomics Inc.<br />
# Pinter , Csaba ; Queens University<br />
# Rankin , Adam ; Robarts Research Institute<br />
# Ross , James ; Brigham and Womens Hospital<br />
# San Jose , Raul ; Brigham and Womens Hospital<br />
# Tokuda , Junichi ; Brigham and Womens Hospital<br />
# Wang , Bo ; SCI Institute University of Utah</div>Amas