https://www.na-mic.org/w/api.php?action=feedcontributions&user=Mt&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T10:23:48ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=919352016 Winter Project Week/Projects/BatchImageAnalysis2016-01-08T06:43:29Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
[[File:LungCT-3DSIFT.png|200px|thumb|left|3D SIFT Lung Features]]<br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
<br />
* Kalli Retzepi (MGH)<br />
* Yangming Ou (MGH)<br />
* Matt Toews (ETS)<br />
* Steve Pieper (BWH)<br />
* Sandy Wells (BWH)<br />
* Randy Gollub (MGH)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Run feature detection code over a collection of medical images pulled from PACS<br />
* Investigate a collection of ADC maps of neonates (diffusion MR)<br />
* Patients labeled with age and health status (normal, mildly abnormal, severely abnormal)<br />
* Use 3D SIFT code to see if health status can be detected in images<br />
* (if time) try text analysis of radiology reports<br />
|<br />
<!-- Add a bulleted list of key points --><br />
* Use deidentified cohort of neonate images collected from MGH<br />
* Install data and software on AWS, try StarCluster<br />
* Explore visualization options <br />
* (if time) integrate image features with analysis of radiology report text<br />
|<br />
<!-- Fill this out at the end of Project Week; describe what you did this week and what you plan to do next --><br />
<br />
Algorithm<br />
<br />
* feature extraction (20 seconds per image)<br />
<br />
* Feature matching O(log N) indexing (< 1 second per image)<br />
<br />
* 3D SIFT-Rank code (Windows, Linux, Max) and read me<br />
http://www.matthewtoews.com/fba/featExtract1.5.zip<br />
<br />
Result<br />
Baseline HIE classification rate: 73%, leave-one-out moderate vs normal.<br />
<br />
<br />
Data<br />
231 subjects, Apparent Diffusion Coefficient (ADC) images.<br />
<br />
|}<br />
<br />
==Features Extracted in ADC MRI Volume ==<br />
<br />
http://wiki.na-mic.org/Wiki/images/b/b2/Image_%282%29.png</div>Mthttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=919342016 Winter Project Week/Projects/BatchImageAnalysis2016-01-08T06:40:21Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
[[File:LungCT-3DSIFT.png|200px|thumb|left|3D SIFT Lung Features]]<br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
<br />
* Kalli Retzepi (MGH)<br />
* Yangming Ou (MGH)<br />
* Matt Toews (ETS)<br />
* Steve Pieper (BWH)<br />
* Sandy Wells (BWH)<br />
* Randy Gollub (MGH)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Run feature detection code over a collection of medical images pulled from PACS<br />
* Investigate a collection of ADC maps of neonates (diffusion MR)<br />
* Patients labeled with age and health status (normal, mildly abnormal, severely abnormal)<br />
* Use 3D SIFT code to see if health status can be detected in images<br />
* (if time) try text analysis of radiology reports<br />
|<br />
<!-- Add a bulleted list of key points --><br />
* Use deidentified cohort of neonate images collected from MGH<br />
* Install data and software on AWS, try StarCluster<br />
* Explore visualization options <br />
* (if time) integrate image features with analysis of radiology report text<br />
|<br />
<!-- Fill this out at the end of Project Week; describe what you did this week and what you plan to do next --><br />
<br />
Algorithm<br />
<br />
* feature extraction (20 seconds per image)<br />
<br />
* feature matching O(log N) indexing (< 1 second per image)<br />
<br />
* 3D SIFT-Rank code (Windows, Linux, Max) and read me<br />
http://www.matthewtoews.com/fba/featExtract1.5.zip<br />
<br />
Leave-one-out classification rate for HIE: moderate vs normal: 73%<br />
<br />
Data<br />
231 subjects, Apparent Diffusion Coefficient (ADC) images.<br />
<br />
|}<br />
<br />
==Features Extracted in ADC MRI Volume ==<br />
<br />
http://wiki.na-mic.org/Wiki/images/b/b2/Image_%282%29.png</div>Mthttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=919332016 Winter Project Week/Projects/BatchImageAnalysis2016-01-08T06:39:38Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
[[File:LungCT-3DSIFT.png|200px|thumb|left|3D SIFT Lung Features]]<br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
<br />
* Kalli Retzepi (MGH)<br />
* Yangming Ou (MGH)<br />
* Matt Toews (ETS)<br />
* Steve Pieper (BWH)<br />
* Sandy Wells (BWH)<br />
* Randy Gollub (MGH)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Run feature detection code over a collection of medical images pulled from PACS<br />
* Investigate a collection of ADC maps of neonates (diffusion MR)<br />
* Patients labeled with age and health status (normal, mildly abnormal, severely abnormal)<br />
* Use 3D SIFT code to see if health status can be detected in images<br />
* (if time) try text analysis of radiology reports<br />
|<br />
<!-- Add a bulleted list of key points --><br />
* Use deidentified cohort of neonate images collected from MGH<br />
* Install data and software on AWS, try StarCluster<br />
* Explore visualization options <br />
* (if time) integrate image features with analysis of radiology report text<br />
|<br />
<!-- Fill this out at the end of Project Week; describe what you did this week and what you plan to do next --><br />
<br />
Algorithm<br />
<br />
* feature extraction (20 seconds per image)<br />
<br />
* feature matching O(log N) indexing (< 1 second per image)<br />
<br />
* code (Windows, Linux, Max) and read me<br />
http://www.matthewtoews.com/fba/featExtract1.5.zip<br />
<br />
Leave-one-out classification rate for HIE: moderate vs normal: 73%<br />
<br />
Data<br />
231 subjects, Apparent Diffusion Coefficient (ADC) images.<br />
<br />
|}<br />
<br />
==Features Extracted in ADC MRI Volume ==<br />
<br />
http://wiki.na-mic.org/Wiki/images/b/b2/Image_%282%29.png</div>Mthttps://www.na-mic.org/w/index.php?title=File:Image_(2).png&diff=91932File:Image (2).png2016-01-08T06:35:39Z<p>Mt: 3D SIFT-Rank features (red spheres) extracted in an ADC volumes.</p>
<hr />
<div>3D SIFT-Rank features (red spheres) extracted in an ADC volumes.</div>Mthttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=919312016 Winter Project Week/Projects/BatchImageAnalysis2016-01-08T06:33:33Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
[[File:LungCT-3DSIFT.png|200px|thumb|left|3D SIFT Lung Features]]<br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
<br />
* Kalli Retzepi (MGH)<br />
* Yangming Ou (MGH)<br />
* Matt Toews (ETS)<br />
* Steve Pieper (BWH)<br />
* Sandy Wells (BWH)<br />
* Randy Gollub (MGH)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Run feature detection code over a collection of medical images pulled from PACS<br />
* Investigate a collection of ADC maps of neonates (diffusion MR)<br />
* Patients labeled with age and health status (normal, mildly abnormal, severely abnormal)<br />
* Use 3D SIFT code to see if health status can be detected in images<br />
* (if time) try text analysis of radiology reports<br />
|<br />
<!-- Add a bulleted list of key points --><br />
* Use deidentified cohort of neonate images collected from MGH<br />
* Install data and software on AWS, try StarCluster<br />
* Explore visualization options <br />
* (if time) integrate image features with analysis of radiology report text<br />
|<br />
<!-- Fill this out at the end of Project Week; describe what you did this week and what you plan to do next --><br />
<br />
Algorithm<br />
<br />
* feature extraction (20 seconds per image)<br />
<br />
* feature matching O(log N) indexing (< 1 second per image)<br />
<br />
* code (Windows, Linux, Max) and read me<br />
http://www.matthewtoews.com/fba/featExtract1.5.zip<br />
<br />
Leave-one-out classification rate for HIE: moderate vs normal: 73%<br />
<br />
Data<br />
231 subjects, Apparent Diffusion Coefficient (ADC) images.<br />
<br />
<br />
<br />
|}</div>Mthttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Dinner&diff=917572016 Winter Project Week/Dinner2016-01-06T17:37:48Z<p>Mt: /* RSVPs */</p>
<hr />
<div><br />
==Dinner Specs==<br />
<br />
*Date and Time: Thursday, January 7th, 6pm<br />
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from Project Week)<br />
*Food: Indian. (Veg and non-veg options, naan, rice)<br />
*Cost: $25 to be paid in cash when you get to the restaurant (for BWH attendees, this is reimbursable)<br />
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks - alcohol or otherwise<br />
<br />
<b>Disclaimer</b>: We went yesterday (Monday) and they were not serving alcohol. - Adam Rankin<br />
<br />
==RSVPs==<br />
#Tina Kapur<br />
#Ron Kikinis<br />
#Steve Pieper<br />
# Andrey Fedorov<br />
# Sonia Pujol<br />
#Hans Meine<br />
#Michael Onken<br />
# Junichi Tokuda<br />
# Dan Blezek<br />
# Beatriz Paniagua<br />
# Johan Andruejol<br />
# Christian Askeland<br />
# Lucia Cevidanes<br />
# Fan Zhang<br />
# Pegah Kahali<br />
# Simon Drouin<br />
# Thomas Kirchner<br />
# Janek Groehl<br />
# Andras Lasso<br />
# Adam Rankin<br />
# Kyle Sunderland<br />
# Csaba Pinter<br />
# Isaiah Norton<br />
# Beatriz Paniagua <br />
# Beatriz Panigua Friend<br />
# Jean-Christophe Fillion-Robin<br />
# Matthew Toews</div>Mthttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=916262016 Winter Project Week/Projects/BatchImageAnalysis2016-01-04T19:08:16Z<p>Mt: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
[[File:LungCT-3DSIFT.png|200px|thumb|left|3D SIFT Lung Features]]<br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
<br />
* Kalli Retzepi (MGH)<br />
* Yangming Ou (MGH)<br />
* Matt Toews (ETS)<br />
* Steve Pieper (BWH)<br />
* Sandy Wells (BWH)<br />
* Randy Gollub (MGH)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Run feature detection code over a collection of medical images pulled from PACS<br />
* Investigate a collection of ADC maps of neonates (diffusion MR)<br />
* Patients labeled with age and health status (normal, mildly abnormal, severely abnormal)<br />
* Use 3D SIFT code to see if health status can be detected in images<br />
* (if time) try text analysis of radiology reports<br />
|<br />
<!-- Add a bulleted list of key points --><br />
* Use deidentified cohort of neonate images collected from MGH<br />
* Install data and software on AWS, try StarCluster<br />
* Explore visualization options <br />
* (if time) integrate image features with analysis of radiology report text<br />
|<br />
<!-- Fill this out at the end of Project Week; describe what you did this week and what you plan to do next --><br />
*<br />
|}</div>Mthttps://www.na-mic.org/w/index.php?title=File:LungCT-3DSIFT.png&diff=91624File:LungCT-3DSIFT.png2016-01-04T19:03:22Z<p>Mt: </p>
<hr />
<div></div>Mthttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Projects/BatchImageAnalysis&diff=915242016 Winter Project Week/Projects/BatchImageAnalysis2016-01-04T05:11:42Z<p>Mt: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2016.png|link=2016_Winter_Project_Week#Projects|[[2016_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
<!-- Add a bulleted list of investigators and their institutions here --><br />
<br />
* Kalli Retzepi (MGH)<br />
* Yangming Ou (MGH)<br />
* Matt Toews (ETS)<br />
* Steve Pieper (BWH)<br />
* Sandy Wells (BWH)<br />
* Randy Gollub (MGH)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Run feature detection code over a collection of medical images pulled from PACS<br />
* Investigate a collection of ADC maps of neonates (diffusion MR)<br />
* Patients labeled with age and health status (normal, mildly abnormal, severely abnormal)<br />
* Use 3D SIFT code to see if health status can be detected in images<br />
* (if time) try text analysis of radiology reports<br />
|<br />
<!-- Add a bulleted list of key points --><br />
* Use deidentified cohort of neonate images collected from MGH<br />
* Install data and software on AWS, try StarCluster<br />
* Explore visualization options <br />
* (if time) integrate image features with analysis of radiology report text<br />
|<br />
<!-- Fill this out at the end of Project Week; describe what you did this week and what you plan to do next --><br />
*<br />
|}</div>Mthttps://www.na-mic.org/w/index.php?title=2016_Winter_Project_Week/Breakout_Sessions/Ultrasound&diff=912152016 Winter Project Week/Breakout Sessions/Ultrasound2015-12-19T18:15:15Z<p>Mt: /* Breakout Session: Ultrasound */</p>
<hr />
<div>=Breakout Session: Ultrasound=<br />
<br />
Each group will present their projects, clinical applications, and plans related to ultrasound-guided interventions.<br />
Available time is 75 minutes in total - about 10 minutes+questions for each group. If you need more time (for demo, etc) then change the allocated time below.<br />
<br />
* BWH - Matt [10 min]<br />
* PerkLab (PerkLab, Queen's University) - Andras [10 min + 5 min demo]<br />
** Includes ultrasound-guided EM-navigated breast lumpectomy demo on a phantom<br />
* SINTEF - Christian [10 min]<br />
* McGill/MNI - Simon [10 min]<br />
* Western - Adam [10 min]<br />
* MITK - Thomas/Janek [10 min]</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=900642015 Summer Project Week:BigDataFeatures2015-06-24T15:17:35Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
* Utsav Pardasani, Robarts (Observing!)<br />
* Salvatore Scaramuzzino (Interested!)<br />
* Andrey Fedorov, BWH<br />
<br />
==3D SIFT-Rank Visualization, SLC 2015, IPMI 2015 ==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
1) Discussed applications of 3D SIFT-Rank <br />
* Analyzing COPD - lung CT - Raul San Jose Estepar<br />
* Identifying similar cases - general MR/CT/US - Tobias Penzkofer<br />
* Infant brain analysis - brain MR - Steve Pieper<br />
* Prostate segmentation - MR/US - Andrey Federov, Salvatore Scaramuzzino<br />
* Astronomical galaxy classification - radio data cube (lambda=21cm) - Davide Punzo<br />
2) Coding for kernel regression framework (C++)<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=900322015 Summer Project Week:BigDataFeatures2015-06-24T15:01:38Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
* Utsav Pardasani, Robarts (Observing!)<br />
* Salvatore Scaramuzzino (Interested!)<br />
* Andrey Fedorov, BWH<br />
<br />
==3D SIFT-Rank Visualization, SLC 2015, IPMI 2015 ==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
1) Discussed applications of 3D SIFT-Rank <br />
* Analyzing COPD - lung CT - Raul San Jose Estepar<br />
* Identifying similar cases - general MR/CT/US - Tobias Penzkofer<br />
* Infant brain analysis - brain MR - Steve Pieper<br />
* Prostate segmentation - MR/US - Andrey Federov<br />
* Astronomical galaxy classification - radio data cube (lambda=21cm) - Davide Punzo<br />
2) Coding for kernel regression framework (C++)<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=899952015 Summer Project Week:BigDataFeatures2015-06-24T14:48:48Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
* Utsav Pardasani, Robarts (Observing!)<br />
* Salvatore Scaramuzzino (Interested!)<br />
* Andrey Fedorov, BWH<br />
<br />
==3D SIFT-Rank Visualization, SLC 2015, IPMI 2015 ==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
1) Discussed applications of 3D SIFT-Rank <br />
* Analyzing COPD - lung CT - Raul San Jose Estepar<br />
* Identifying similar cases - MR/CT - Tobias Penzkofer<br />
* Infant brain analysis - MR - Steve Pieper<br />
* Prostate segmentation - MR/US - Andrey Federov<br />
* Galaxy classification - Astronomical Radio Data Cube (lambda=21cm) - Davide Punzo<br />
2) Coding for kernel regression framework (C++)<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=899802015 Summer Project Week:BigDataFeatures2015-06-24T14:45:13Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
* Utsav Pardasani, Robarts (Observing!)<br />
* Salvatore Scaramuzzino (Interested!)<br />
* Andrey Fedorov, BWH<br />
<br />
==3D SIFT-Rank Visualization, SLC 2015, IPMI 2015 ==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
1) Discussed applications of 3D SIFT-Rank <br />
* Analyzing COPD - lung CT - Raul San Jose Estepar<br />
* Identifying similar cases - MR/CT - Tobias Penzkofer<br />
* Infant brain analysis - MR - Steve Pieper<br />
* Prostate segmentation - MR/US - Andrey Federov<br />
* Galaxy classification - Astronomical Radio Data Cube (lambda=21cm) - Davide Punzo<br />
2) Developing kernel regression framework (C++)<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=899452015 Summer Project Week:BigDataFeatures2015-06-24T14:08:10Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
* Utsav Pardasani, Robarts (Observing!)<br />
* Salvatore Scaramuzzino (Interested!)<br />
* Andrey Fedorov, BWH<br />
<br />
==3D SIFT-Rank Visualization, SLC 2015, IPMI 2015 ==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
Discussion of Potential Applications <br />
* Analyzing COPD - lung CT - Raul San Jose Estepar<br />
* Identifying similar cases - MR/CT - Tobias Penzkofer<br />
* Infant brain analysis - MR - Steve Pieper<br />
* Prostate segmentation - MR/US - Andrey Federov<br />
* Galaxy classification - Astronomical Radio Data Cube (lambda=21cm) - Davide Punzo<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=899432015 Summer Project Week:BigDataFeatures2015-06-24T13:59:56Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
* Utsav Pardasani, Robarts (Observing!)<br />
* Salvatore Scaramuzzino (Interested!)<br />
* Andrey Fedorov, BWH<br />
<br />
==3D SIFT-Rank Visualization, SLC 2015, IPMI 2015 ==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
Discussion of Potential Applications <br />
- Analyzing COPD - lung CT - Raul San Jose Estepar<br />
- Identifying similar cases - MR/CT - Tobias Penzkofer<br />
- Infant brain analysis - MR - Steve Pieper<br />
- Prostate segmentation - MR/US - Andrey Federov<br />
- Galaxy classification - Astronomical Radio Data Cube (lambda=21cm) - Davide Punzo<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week&diff=897832015 Summer Project Week2015-06-22T10:00:55Z<p>Mt: /* Feature Based Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-Summer2015.png|300px]]<br />
<br><br />
<br />
<br />
<br />
'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' June 21-24, 2015.<br />
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]<br />
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page<br />
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.<br />
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])<br />
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Sunday, June 21 <br />
!style="width:18%" |Monday, June 22 <br> Room Berlin <br />
!style="width:18%" |Tuesday, June 23 <br> Room Berlin <br />
!style="width:18%" |Wednesday, June 24 <br> Room Berlin <br />
|-<br />
|bgcolor="#ffffdd"|'''9:00am-3:00pm:'''<br />
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby<br />
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br><br />
'''11am-3pm''' <font color="#503020">Work <br><br />
<br />
|<br />
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br><br />
'''11am-3pm''' <font color="#503020">Work<br />
| <font color="#503020">Work <br><br />
|-<br />
|bgcolor="#ffffdd"|'''2:00pm-4:00pm'''<br />
|bgcolor="#ffffaa"|Lunch <br> [[Barcelona Restaurants|Places to Eat]] <br />
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]] <br />
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]] <br />
|-<br />
|bgcolor="#ffffdd"|'''4:00-7:00pm'''<br />
|<font color="#503020"> Work<br />
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper) <br>4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges. <br><br />
|'''4:00-5:00pm:''' <font color="#503020"> Work <br><br />
'''5:00-6pm:''' Report Progress<br />
|-<br />
|bgcolor="#ffffdd"|'''7:00pm'''<br />
|bgcolor="#f0e68b"|<br />
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]] <br />
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]] <br />
|bgcolor="#f0e68b"|'''6:00pm''' Adjourn Project Week and relocate to CARS Opening<br> '''7:30pm''' CARS Welcome Reception <br />
|}<br />
<br />
*Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.<br />
*Here is a list of [[Barcelona Restaurants | locally recommended places to eat]] in the vicinity of the conference hotel. All participants are responsible for their own meals.<br />
<br />
== '''Background''' ==<br />
<br />
<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 researchers from around the world. 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], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program]. <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 />
The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].<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 />
=Projects=<br />
* [[2015_Summer_Project_Week_Template | Template for project pages]]<br />
<br />
<br />
==Equipment==<br />
<br />
*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)<br />
<br />
==Image-Guided Therapy==<br />
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas, Andras, Jay, Steve, Alvaro, Javier, Adam, Caroline, Noby)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)<br />
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov, Adam Rankin)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, David García, Javier Pascau)<br />
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]<br />
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)<br />
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)<br />
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)<br />
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)<br />
*[[2015_Summer_Project_Week:SlicerTAVI | SlicerTAVI ]] (Adam Rankin)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]<br />
*[[2015_Summer_Project_Week:OpenSource_MRTRUS_Fusion_for_Prostate_biopsy|Open-source MRI-TRUS Fusion for Prostate biopsy]] (Andrey Fedorov, Andras Lasso, Clare Tempany)<br />
*[[2015_Summer_Project_Week:TrackerlessMRIUSFusion | Trackerless MRI - US Registration ]] (Utsav Pardasani)<br />
<br />
==Feature Based Image Analysis==<br />
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells, Clara Meinzer)<br />
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Matthew Toews, Tina Kapur)<br />
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)<br />
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)<br />
<br />
==Chest Imaging Platform==<br />
*[[2015_Summer_Project_Week:Slicer_CIP | Slicer CIP: advanced features and deployment ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva)<br />
*[[2015_Summer_Project_Week:PAA_Ratio | PAA Ratio Module ]] (Jorge Onieva,Raúl San José)<br />
*[[2015_Summer_Project_Week:Tracheal_Stent_Planning | Planning for tracheal stents ]] (Raúl San José, Jorge Onieva, George Cheng)<br />
<br />
==QIICR==<br />
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast (DSC) MRI for brain ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)<br />
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for Dynamic Contrast Enhanced (DCE) MRI ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)<br />
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)<br />
<br />
==Infrastructure==<br />
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)<br />
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin,Hans Meine)<br />
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Franklin King)<br />
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, Utsav Pardasani)<br />
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)<br />
*[[2015_Summer_Project_Week:Slicer_Conda | Integrate Conda Python in Slicer]] (Jorge Onieva, Raúl San José, Utsav Pardasani, Steve Pieper)<br />
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)<br />
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC, Steve Pieper)<br />
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, Steve Pieper, Nicolas Rannou)<br />
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)<br />
<br />
==Web==<br />
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Michael Onken, Steve Pieper)<br />
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)<br />
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)<br />
*[[2015_Summer_Project_Week:SlicerCardboard| Slicer for mobile-based vr goggles]] (Utsav Pardasani, Adam Rankin)<br />
<br />
==Astronomy==<br />
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)<br />
<br />
== '''Registrants''' ==<br />
<br />
Please add your name to the list. This is the registration mechanism for this project week.<br />
#Tina Kapur, BWH<br />
#Ron Kikinis, BWH & Fraunhofer<br />
#Steve Pieper, Isomics<br />
#Tamas Ungi, Queen's University, Canada<br />
#Andras Lasso, Queen's University, Canada<br />
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy<br />
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy<br />
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy<br />
#Nicole Aucoin, BWH<br />
#Sonia Pujol, BWH<br />
#Dženan Zukić, Kitware, Carrboro, NC<br />
#Jayender Jagadeesan, BWH<br />
#Guido Gerig, Utah<br />
#Sandy Wells, BWH<br />
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada<br />
#Frank Preiswerk, BWH<br />
#Raul San Jose, BWH<br />
#Jorge Onieva, BWH<br />
#Yulong Zhao, Université de Rennes<br />
#Laurent Chauvin, BWH<br />
#Michael Onken, Open Connections<br />
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany<br />
#Javier Pascau, Universidad Carlos III de Madrid, Spain<br />
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain<br />
#Nobuhiko Hata, BWH<br />
#Robert H. Owen, BK Medical ApS, Denmark<br />
#Clare Tempany, BWH<br />
#Adam Rankin, Robarts<br />
#Utsav Pardasani, Robarts<br />
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico<br />
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico<br />
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands<br />
#Andrey Fedorov, BWH<br />
#Nicolas Rannou, BCH<br />
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain<br />
#Laura Sanz, Universidad Carlos III de Madrid, Spain<br />
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain<br />
#David García, Universidad Carlos III de Madrid, Spain<br />
#Franklin King, Queen's University / BWH<br />
#Jorge García, Universidad Politécnica de Madrid, Spain<br />
#Peter Behringer, BWH<br />
#Caroline Essert, University of Strasbourg<br />
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany<br />
#Matthew Holden, Queen's University, Canada<br />
#Sara Fernandez Vidal, ICM, France<br />
#Laszlo Kanyasi, Perk Lab affiliate, Hungary<br />
#Xiao Da, MGH<br />
#Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium<br />
#Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium<br />
#Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium<br />
#Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium<br />
#Clara Meinzer, Semmelweis University, Hungary<br />
#Yves Martelli, Galgo Medical, Barcelona, Spain<br />
#Alvaro Gomez (Universidad de la Republica, Uruguay)</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=897612015 Summer Project Week:BigDataFeatures2015-06-22T09:21:58Z<p>Mt: /* Previous Work: 3D SIFT-Rank Visualization, SLC 2015 */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
<br />
==3D SIFT-Rank Visualization, SLC 2015, IPMI 2015 ==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=897582015 Summer Project Week:BigDataFeatures2015-06-22T09:19:09Z<p>Mt: /* Previous Work: 3D SIFT-Rank Visualization, SLC 2015 */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
<br />
==Previous Work: 3D SIFT-Rank Visualization, SLC 2015==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=897322015 Summer Project Week:BigDataFeatures2015-06-22T09:03:34Z<p>Mt: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
<br />
==Previous Work: 3D SIFT-Rank Visualization, SLC 2015==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.<br><br />
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=897192015 Summer Project Week:BigDataFeatures2015-06-22T08:55:02Z<p>Mt: /* Previous Work: 3D SIFT-Rank Visualization, SLC 2015 */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
<br />
==Previous Work: 3D SIFT-Rank Visualization, SLC 2015==<br />
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=File:Lung-ct.png&diff=89716File:Lung-ct.png2015-06-22T08:52:59Z<p>Mt: </p>
<hr />
<div></div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=897032015 Summer Project Week:BigDataFeatures2015-06-22T08:47:57Z<p>Mt: /* Previous Work: 3D SIFT-Rank Visualization, SLC 2015 */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
<br />
==Previous Work: 3D SIFT-Rank Visualization, SLC 2015==<br />
[[File:3D_SIFT_Lung.png|400px|thumb|left|Lung CT]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US]]<br />
[[File:Img-feat.png|300px|thumb|left|Data Reduction]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=File:Img-feat.png&diff=89697File:Img-feat.png2015-06-22T08:46:20Z<p>Mt: </p>
<hr />
<div></div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=896292015 Summer Project Week:BigDataFeatures2015-06-22T07:10:05Z<p>Mt: /* 3D SIFT-Rank Visualization - SLC 2015 */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
<br />
==Previous Work: 3D SIFT-Rank Visualization, SLC 2015==<br />
[[File:3D_SIFT_Lung.png|400px|thumb|left|Lung CT]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=896282015 Summer Project Week:BigDataFeatures2015-06-22T07:09:23Z<p>Mt: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
<br />
==3D SIFT-Rank Visualization - SLC 2015==<br />
[[File:3D_SIFT_Lung.png|400px|thumb|left|Lung CT]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week&diff=894882015 Summer Project Week2015-06-11T17:38:48Z<p>Mt: /* Feature Based Image Analysis */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-Summer2015.png|300px]]<br />
<br><br />
<br />
<br />
<br />
'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' June 21-24, 2015.<br />
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]<br />
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page<br />
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.<br />
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])<br />
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Sunday, June 21<br />
!style="width:18%" |Monday, June 22<br />
!style="width:18%" |Tuesday, June 23<br />
!style="width:18%" |Wednesday, June 24<br />
|-<br />
|bgcolor="#ffffdd"|'''10:00am-3:00pm:'''<br />
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby<br />
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br><br />
'''11am-3pm''' <font color="#503020">Work <br><br />
<br />
|<br />
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br><br />
'''11am-3pm''' <font color="#503020">Work<br />
|'''10am-3pm''' <font color="#503020">Work <br><br />
|-<br />
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|-<br />
|bgcolor="#ffffdd"|'''5:00-7:00pm'''<br />
|'''5:00-7pm:''' <font color="#503020"> Work<br />
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper)<br />
|'''5:00-6pm:''' <font color="#503020"> Work <br><br />
'''6:00-7pm:''' Report Progress<br />
|-<br />
|bgcolor="#ffffdd"|'''7:00pm'''<br />
|bgcolor="#f0e68b"|<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|}<br />
<br />
== '''Background''' ==<br />
<br />
<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 researchers from around the world. 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], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program]. <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 />
The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].<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 />
=Projects=<br />
* [[2015_Summer_Project_Week_Template | Template for project pages]]<br />
<br />
<br />
==Equipment==<br />
<br />
*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)<br />
<br />
==Image-Guided Therapy==<br />
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]<br />
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]<br />
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)<br />
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)<br />
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, Javier Pascau)<br />
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)<br />
<br />
==Feature Based Image Analysis==<br />
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells)<br />
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)<br />
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)<br />
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)<br />
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)<br />
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)<br />
<br />
==Astronomy==<br />
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)<br />
<br />
==Infrastructure==<br />
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)<br />
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)<br />
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC, Steve Pieper)<br />
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, Steve Pieper, Nicolas Rannou)<br />
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)<br />
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller, Hans Meine)<br />
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Franklin King, BWH)<br />
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, BWH)<br />
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)<br />
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov)<br />
<br />
==Web==<br />
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Michael Onken, Steve Pieper)<br />
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)<br />
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)<br />
<br />
==QIICR==<br />
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast MRI (DSC) for brain ]] (Xiao Da)<br />
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for DCE ]] (Xiao Da)<br />
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)<br />
<br />
== '''Registrants''' ==<br />
<br />
Please add your name to the list. This is the registration mechanism for this project week.<br />
#Tina Kapur, BWH<br />
#Ron Kikinis, BWH & Fraunhofer<br />
#Steve Pieper, Isomics<br />
#Tamas Ungi, Queen's University, Canada<br />
#Andras Lasso, Queen's University, Canada<br />
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy<br />
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy<br />
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy<br />
#Hans Meine, Fraunhofer MEVIS, Bremen, Germany<br />
#Nicole Aucoin, BWH<br />
#Sonia Pujol, BWH<br />
#Dženan Zukić, Kitware, Carrboro, NC<br />
#Jayender Jagadeesan, BWH<br />
#Guido Gerig, Utah<br />
#Sandy Wells, BWH<br />
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada<br />
#Frank Preiswerk, BWH<br />
#Junichi Tokuda, BWH<br />
#Raul San Jose, BWH<br />
#Jorge Onieva, BWH<br />
#Yulong Zhao, Université de Rennes<br />
#Laurent Chauvin, BWH<br />
#Michael Onken, Open Connections<br />
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany<br />
#Javier Pascau, Universidad Carlos III de Madrid, Spain<br />
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain<br />
#Nobuhiko Hata, BWH<br />
#Robert H. Owen, BK Medical ApS, Denmark<br />
#Clare Tempany, BWH<br />
#Adam Rankin, Robarts<br />
#Utsav Pardasani, Robarts<br />
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico<br />
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico<br />
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands<br />
#Andrey Fedorov, BWH<br />
#Nicolas Rannou, BCH<br />
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain<br />
#Laura Sanz, Universidad Carlos III de Madrid, Spain<br />
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain<br />
#David García, Universidad Carlos III de Madrid, Spain<br />
#Franklin King, Queen's University / BWH<br />
#Jorge García, Universidad Politécnica de Madrid, Spain<br />
#Peter Behringer, BWH<br />
#Caroline Essert, University of Strasbourg<br />
#Pradyumna Reddy, Birla Institute of Technology and Science, Goa-Campus, India.<br />
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany<br />
#Matthew Holden, Queen's University, Canada</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=894872015 Summer Project Week:BigDataFeatures2015-06-11T17:38:19Z<p>Mt: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Raul San Jose Estepar, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=893742015 Summer Project Week:BigDataFeatures2015-06-09T17:15:28Z<p>Mt: /* References */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<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 />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==<br />
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br><br />
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III. <br />
Information Processing in Medical Imaging (IPMI), 2015.</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=893462015 Summer Project Week:BigDataFeatures2015-06-05T17:48:45Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<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 />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=893452015 Summer Project Week:BigDataFeatures2015-06-05T17:47:53Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<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 />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical domains: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
** Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
** Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=893442015 Summer Project Week:BigDataFeatures2015-06-05T17:47:33Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<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 />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Technology: invariant feature extraction, descriptor representation.<br />
* Application domains: registration, segmentation, classification.<br />
* Image domains: lung CT, brain MR, prostate and brain ultrasound.<br />
* Clinical domains: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion and documentation<br />
- Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).<br />
- Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=893432015 Summer Project Week:BigDataFeatures2015-06-05T17:43:39Z<p>Mt: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<br />
* Tina Kapur, BWH, Harvard Medical School<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 />
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.<br />
* Example image domains: lung CT, brain MR.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Discussion of algorithms: fast KNN methods, hashing.<br />
* Discussion of mathematical formalisms: probabilistic inference, kernel methods.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div><br />
<br />
==References==</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=889522015 Summer Project Week:BigDataFeatures2015-03-30T12:52:22Z<p>Mt: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<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><br />
<br />
==References==</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week:BigDataFeatures&diff=889512015 Summer Project Week:BigDataFeatures2015-03-30T12:51:12Z<p>Mt: Created page with '__NOTOC__ <gallery> Image:PW-Summer2015.png|Projects List </gallery> ==Key Investigators== * Matthew Toews, École de Technologie Supérieu…'</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews, École de Technologie Supérieure<br />
* William Wells, BWH, Harvard Medical School<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 style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>References</h3><br />
*<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week&diff=889502015 Summer Project Week2015-03-30T12:50:43Z<p>Mt: /* Registrants */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-Summer2015.png|300px]]<br />
<br><br />
<br />
<br />
==Logistics==<br />
<br />
Location: NH COLLECTION CONSTANZA Hotel, Barcelona<br />
<br />
Dates:<br />
<br />
*Start: Sunday, June 21st (early evening start with project presentations)<br />
**3 days of work: Monday June 22, Tuesday June 23, Wednesday June 24<br />
*Adjourn: Wednesday June 24th at 5pm<br />
<br />
Registration Fee: zero. We will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.<br />
<br />
== '''Background''' ==<br />
<br />
<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 event in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Barcelona, Spain] in June 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 />
=Projects=<br />
* [[2015_Summer_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
*[[2015 Orthognatic Surgery|Orthognatic Surgery]]<br />
<br />
==Huntington's Disease==<br />
==TBI==<br />
<br />
==Stroke==<br />
<br />
==Cardiac==<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
<br />
==[http://qiicr.org QIICR]==<br />
<br />
==Feature Extraction==<br />
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]<br />
<br />
==Slicer4 Extensions==<br />
<br />
==TMJOA RO1 - Collaboration with NAMIC==<br />
<br />
==Infrastructure==<br />
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)<br />
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC)<br />
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, ??)<br />
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)<br />
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 21-24, 2015.<br />
*'''Location:''' Barcelona, Spain<br />
*'''REGISTRATION:''' 0<br />
*'''Registration Fee:''' TBD<br />
*'''Hotel:''' TBD<br />
*'''Room sharing''': If interested, add your name to the list: [[2015_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
Please add your name to the list. This is the registration mechanism for this project week.<br />
<br />
#Tina Kapur<br />
#Ron Kikinis<br />
#Steve Pieper<br />
#Tamas Ungi (Queen's University, Canada)<br />
#Paolo Zaffino (ImagEngLab, Magna Graecia University, Italy)<br />
#Salvatore Scaramuzzino (ImagEngLab, Magna Graecia University, Italy)<br />
#Giampaolo Pileggi (ImagEngLab, Magna Graecia University, Italy)<br />
#Hans Meine (Fraunhofer MEVIS, Bremen, Germany)<br />
#Nicole Aucoin (BWH)<br />
#Sonia Pujol (BWH)<br />
#Dženan Zukić (Kitware, Carrboro, NC, USA)<br />
#Jayender Jagadeesan (BWH)<br />
#Guido Gerig<br />
#Matthew Toews (École de Technologie Supérieure, Montreal, Canada)</div>Mthttps://www.na-mic.org/w/index.php?title=2015_Summer_Project_Week&diff=889492015 Summer Project Week2015-03-30T12:46:50Z<p>Mt: /* Feature Extraction */</p>
<hr />
<div>__NOTOC__<br />
<br />
[[image:PW-Summer2015.png|300px]]<br />
<br><br />
<br />
<br />
==Logistics==<br />
<br />
Location: NH COLLECTION CONSTANZA Hotel, Barcelona<br />
<br />
Dates:<br />
<br />
*Start: Sunday, June 21st (early evening start with project presentations)<br />
**3 days of work: Monday June 22, Tuesday June 23, Wednesday June 24<br />
*Adjourn: Wednesday June 24th at 5pm<br />
<br />
Registration Fee: zero. We will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.<br />
<br />
== '''Background''' ==<br />
<br />
<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 event in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Barcelona, Spain] in June 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 />
=Projects=<br />
* [[2015_Summer_Project_Week_Template | Template for project pages]]<br />
<br />
==Image-Guided Therapy==<br />
*[[2015 Orthognatic Surgery|Orthognatic Surgery]]<br />
<br />
==Huntington's Disease==<br />
==TBI==<br />
<br />
==Stroke==<br />
<br />
==Cardiac==<br />
<br />
==Chronic Obstructive Pulmonary Disease, Lung, Chest ==<br />
<br />
<br />
==[http://qiicr.org QIICR]==<br />
<br />
==Feature Extraction==<br />
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells)<br />
<br />
==Additional Brain Image Analysis==<br />
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]<br />
<br />
==Slicer4 Extensions==<br />
<br />
==TMJOA RO1 - Collaboration with NAMIC==<br />
<br />
==Infrastructure==<br />
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)<br />
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC)<br />
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, ??)<br />
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with BRAINSFit in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)<br />
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin, Jim Miller)<br />
<br />
== '''Logistics''' ==<br />
<br />
*'''Dates:''' June 21-24, 2015.<br />
*'''Location:''' Barcelona, Spain<br />
*'''REGISTRATION:''' 0<br />
*'''Registration Fee:''' TBD<br />
*'''Hotel:''' TBD<br />
*'''Room sharing''': If interested, add your name to the list: [[2015_Summer_Project_Week/RoomSharing|here]]<br />
<br />
== '''Registrants''' ==<br />
<br />
Please add your name to the list. This is the registration mechanism for this project week.<br />
<br />
#Tina Kapur<br />
#Ron Kikinis<br />
#Steve Pieper<br />
#Tamas Ungi (Queen's University, Canada)<br />
#Paolo Zaffino (ImagEngLab, Magna Graecia University, Italy)<br />
#Salvatore Scaramuzzino (ImagEngLab, Magna Graecia University, Italy)<br />
#Giampaolo Pileggi (ImagEngLab, Magna Graecia University, Italy)<br />
#Hans Meine (Fraunhofer MEVIS, Bremen, Germany)<br />
#Nicole Aucoin (BWH)<br />
#Sonia Pujol (BWH)<br />
#Dženan Zukić (Kitware, Carrboro, NC, USA)<br />
#Jayender Jagadeesan (BWH)<br />
#Guido Gerig</div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=886503D SIFT VIEW2015-01-09T16:45:38Z<p>Mt: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
==New Visualization==<br />
[[File:3D_SIFT_Lung.png|500px|thumb|left|Lung CT]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US]]<br />
<br />
==Key Investigators==<br />
* Matthew Toews, Raul San Jose, Steve Pieper, Nicole Aucoin, Bill Lorensen, Lauren O'Donnell, Andriy Fedorov, William Wells BWH<br />
<br />
==Code==<br />
3D SIFT feature extraction code http://www.matthewtoews.com/fba/featExtract1.5.zip<br />
<br />
Python conversion code [[Media:3D_SIFT_VISUALIZATION.gz]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Evaluated Slicer fiducials and VTK glyph models for feature display<br />
* Developed a python script to convert a 3D SIFT feature file into a VTK model (thanks Lauren, Nicole)<br />
* ToDo:<br />
** display feature orientation (possibly as another glyph)<br />
** display varying feature opacity<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=886453D SIFT VIEW2015-01-09T16:43:22Z<p>Mt: /* Code */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
==New Visualization==<br />
[[File:3D_SIFT_Lung.png|500px|thumb|left|Lung CT]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US]]<br />
<br />
==Key Investigators==<br />
* Matthew Toews, Raul San Jose, Steve Pieper, Nicole Aucoin, Lauren O'Donnell, Andriy Fedorov, William Wells BWH<br />
<br />
==Code==<br />
3D SIFT feature extraction code http://www.matthewtoews.com/fba/featExtract1.5.zip<br />
<br />
Python conversion code [[Media:3D_SIFT_VISUALIZATION.gz]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Evaluated Slicer fiducials and VTK glyph models for feature display<br />
* Developed a python script to convert a 3D SIFT feature file into a VTK model (thanks Lauren, Nicole)<br />
* ToDo:<br />
** display feature orientation (possibly as another glyph)<br />
** display varying feature opacity<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=886433D SIFT VIEW2015-01-09T16:43:00Z<p>Mt: /* Code */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
==New Visualization==<br />
[[File:3D_SIFT_Lung.png|500px|thumb|left|Lung CT]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US]]<br />
<br />
==Key Investigators==<br />
* Matthew Toews, Raul San Jose, Steve Pieper, Nicole Aucoin, Lauren O'Donnell, Andriy Fedorov, William Wells BWH<br />
<br />
==Code==<br />
3D SIFT feature extraction code <a href="http://www.matthewtoews.com/fba/featExtract1.5.zip"><br />
<br />
Python conversion code [[Media:3D_SIFT_VISUALIZATION.gz]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Evaluated Slicer fiducials and VTK glyph models for feature display<br />
* Developed a python script to convert a 3D SIFT feature file into a VTK model (thanks Lauren, Nicole)<br />
* ToDo:<br />
** display feature orientation (possibly as another glyph)<br />
** display varying feature opacity<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=886403D SIFT VIEW2015-01-09T16:41:46Z<p>Mt: /* Code */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
==New Visualization==<br />
[[File:3D_SIFT_Lung.png|500px|thumb|left|Lung CT]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US]]<br />
<br />
==Key Investigators==<br />
* Matthew Toews, Raul San Jose, Steve Pieper, Nicole Aucoin, Lauren O'Donnell, Andriy Fedorov, William Wells BWH<br />
<br />
==Code==<br />
3D SIFT feature extraction <a href="http://www.matthewtoews.com/fba/featExtract1.5.zip">code</a><br />
<br />
Python conversion code [[Media:3D_SIFT_VISUALIZATION.gz]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Evaluated Slicer fiducials and VTK glyph models for feature display<br />
* Developed a python script to convert a 3D SIFT feature file into a VTK model (thanks Lauren, Nicole)<br />
* ToDo:<br />
** display feature orientation (possibly as another glyph)<br />
** display varying feature opacity<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=885163D SIFT VIEW2015-01-09T00:31:01Z<p>Mt: /* New Visualization */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
==New Visualization==<br />
[[File:3D_SIFT_Lung.png|500px|thumb|left|Lung CT]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US]]<br />
<br />
==Key Investigators==<br />
* Matthew Toews, Raul San Jose, Steve Pieper, Nicole Aucoin, Lauren O'Donnell, Andriy Fedorov, William Wells BWH<br />
<br />
==Code==<br />
Python conversion code [[Media:3D_SIFT_VISUALIZATION.gz]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Evaluated Slicer fiducials and VTK glyph models for feature display<br />
* Developed a python script to convert a 3D SIFT feature file into a VTK model (thanks Lauren, Nicole)<br />
* ToDo:<br />
** display feature orientation (possibly as another glyph)<br />
** display varying feature opacity<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=885153D SIFT VIEW2015-01-09T00:30:35Z<p>Mt: /* Example Visualization */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
==New Visualization==<br />
[[File:3D_SIFT_Lung.png|500px|thumb|left|alt text]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|alt text]]<br />
<br />
==Key Investigators==<br />
* Matthew Toews, Raul San Jose, Steve Pieper, Nicole Aucoin, Lauren O'Donnell, Andriy Fedorov, William Wells BWH<br />
<br />
==Code==<br />
Python conversion code [[Media:3D_SIFT_VISUALIZATION.gz]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Evaluated Slicer fiducials and VTK glyph models for feature display<br />
* Developed a python script to convert a 3D SIFT feature file into a VTK model (thanks Lauren, Nicole)<br />
* ToDo:<br />
** display feature orientation (possibly as another glyph)<br />
** display varying feature opacity<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=885143D SIFT VIEW2015-01-09T00:29:32Z<p>Mt: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
==Example Visualization==<br />
[[File:3D_SIFT_Lung.png|500px|thumb|left|alt text]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|alt text]]<br />
<br />
==Key Investigators==<br />
* Matthew Toews, Raul San Jose, Steve Pieper, Nicole Aucoin, Lauren O'Donnell, Andriy Fedorov, William Wells BWH<br />
<br />
==Code==<br />
Python conversion code [[Media:3D_SIFT_VISUALIZATION.gz]]<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Evaluated Slicer fiducials and VTK glyph models for feature display<br />
* Developed a python script to convert a 3D SIFT feature file into a VTK model (thanks Lauren, Nicole)<br />
* ToDo:<br />
** display feature orientation (possibly as another glyph)<br />
** display varying feature opacity<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=File:3D_SIFT_VISUALIZATION.gz&diff=88513File:3D SIFT VISUALIZATION.gz2015-01-09T00:26:41Z<p>Mt: Python code to visualize 3D SIFT features</p>
<hr />
<div>Python code to visualize 3D SIFT features</div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=885123D SIFT VIEW2015-01-09T00:22:34Z<p>Mt: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
[[File:3D_SIFT_Lung.png|300px|thumb|left|alt text]]<br />
[[File:3D_SIFT_Prostate.png|300px|thumb|left|alt text]]<br />
<br />
==Key Investigators==<br />
* Matthew Toews BWH<br />
* Raul San Jose BWH<br />
* Steve Pieper BWH<br />
* Nicole Aucoin BWH<br />
* Lauren O'Donnell BWH<br />
* Andriy Fedorov, BWH<br />
* William Wells BWH<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Evaluated Slicer fiducials and VTK glyph models for feature display<br />
* Developed a python script to convert a 3D SIFT feature file into a VTK model (thanks Lauren, Nicole)<br />
* ToDo:<br />
** display feature orientation (possibly as another glyph)<br />
** display varying feature opacity<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=File:3D_SIFT_Lung.png&diff=88507File:3D SIFT Lung.png2015-01-09T00:15:00Z<p>Mt: </p>
<hr />
<div></div>Mthttps://www.na-mic.org/w/index.php?title=File:3D_SIFT_Prostate.png&diff=88503File:3D SIFT Prostate.png2015-01-09T00:12:09Z<p>Mt: </p>
<hr />
<div></div>Mthttps://www.na-mic.org/w/index.php?title=3D_SIFT_VIEW&diff=883133D SIFT VIEW2015-01-05T19:09:59Z<p>Mt: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
Image:slicer_lung_features.png|Lung CT, 3D volume visualization<br />
Image:3D_SIFT_BRAIN.png|Brain MR, 2D slice visualization<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Matthew Toews BWH<br />
* Raul San Jose BWH<br />
* Steve Pieper BWH<br />
* Nicole Aucoin BWH<br />
* Andriy Fedorov, BWH<br />
* William Wells BWH<br />
<br />
==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Generate effective visualizations for 3D SIFT feature sets in Slicer.<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Investigate methods for visualizing 3D feature location, scale, orientation and group label (e.g. diseased, healthy)<br />
* Location, scale: spheres (markups), group labels: color/transparency<br />
* Visualization: Slicer Python module based on Slicer Markups<br />
* Data preparation: c++<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
*<br />
</div><br />
</div></div>Mthttps://www.na-mic.org/w/index.php?title=Small_lung_nodule_differential_diagnosis_using_3D_Slicer&diff=88312Small lung nodule differential diagnosis using 3D Slicer2015-01-05T19:08:02Z<p>Mt: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
[[File:LungCT_Slicer_Figure1_Ming_Li.jpg|400px]]<br />
<br />
==Key Investigators==<br />
* Li Ming, MD, Department of Radiology, HuaDong Hospital affiliated to FUDAN University<br />
* Jay Jagadeesan, BWH<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>Mt