https://www.na-mic.org/w/index.php?action=history&feed=atom&title=2010_Summer_Project_Week_Prostate_MRI_Segmentation
2010 Summer Project Week Prostate MRI Segmentation - Revision history
2026-04-05T21:55:36Z
Revision history for this page on the wiki
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https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Prostate_MRI_Segmentation&diff=55137&oldid=prev
Fedorov: /* Key Investigators */
2010-06-24T22:47:21Z
<p><span dir="auto"><span class="autocomment">Key Investigators</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 22:47, 24 June 2010</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><h3>Progress</h3></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><h3>Progress</h3></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">* Evaluated new approach to segmentation developed by Yi Gao. Steps:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># register (up to bspline) each greyscale training image of the same modality to the subject</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># average binary gland segmentations to obtain probability image</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># initialize level set evolution with the voxels of high probability</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># evolve contour under constraint of the spatial prior, intensity and curvature (parameters explored)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">* Testing performed using the atlas constructed using MICCAI'09 challenge data (different field strength) for segmenting intra-procedural MRI w/o er-coil obtained at 3T</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">* Main challenges identified:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># inter-subject registration is very difficult, no robust solution found: this creates problems with initialization of the contour evolution</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># with manual initialization, contour evolution has difficulties since prior is not well-aligned and intensity is highly non-uniform</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">* Future directions:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># incorporate shape constraint into the model</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># consider edges in contour evolution?</ins></div></td></tr>
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Fedorov
https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Prostate_MRI_Segmentation&diff=54239&oldid=prev
Fedorov at 19:14, 16 June 2010
2010-06-16T19:14:14Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:14, 16 June 2010</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Image:prostate1.png|T2w MRI <del class="diffchange diffchange-inline">with prostate gland outlined</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Image:prostate1.png|T2w MRI<ins class="diffchange diffchange-inline">, 1.5T pelvic coil</ins></div></td></tr>
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Fedorov
https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Prostate_MRI_Segmentation&diff=54234&oldid=prev
Fedorov: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List Image:prostate1.png|T2w MRI with prostate gland outlined Image:prostate2.png| </galle…'
2010-06-16T19:09:12Z
<p>Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|<a href="/wiki/2010_Summer_Project_Week#Projects" title="2010 Summer Project Week">Projects List</a> Image:prostate1.png|T2w MRI with prostate gland outlined Image:prostate2.png| </galle…'</p>
<p><b>New page</b></p><div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
Image:prostate1.png|T2w MRI with prostate gland outlined<br />
Image:prostate2.png|<br />
</gallery><br />
<br />
==Key Investigators==<br />
* BWH: Andriy Fedorov<br />
* GaTech: Yi Gao<br />
<br />
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<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
Segmentation of the prostate gland is one of the steps in the planning of intra-operative guidance for image-guided biopsy and brachytherapy procedures. Accurate segmentation of the gland may be important for accurate calculation of the dose distribution in brachytherapy, and can be critical for accurate registration using surface-based approaches. We would like to automate the segmentation process, to reduce processing time, and improve its accuracy and reproducibility.<br />
<br />
We will evaluate the applicability of the prostate segmentation tools developed by Georgia Tech (Yi Gao) on the 1.5T and 3.0T scans with and without endo-rectal coil.<br />
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<h3>Approach, Plan</h3><br />
<br />
This project is a follow-up on the previous developments in projects weeks of 2009-2010 (see references).<br />
<br />
Our plan is to:<br />
* make sure the software is compiled and applied correctly<br />
* review processing pipeline<br />
* evaluate the accuracy of segmentation compared with the manual outlines (we will use the [[2009_prostate_segmentation_challenge_MICCAI | publicly available dataset]] from MICCAI 2009 Prostate segmentation challenge (1.5T) as well as the images from on-going image-guided biopsy program at BWH (3T T2w, Siemens Magnetom)<br />
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</div><br />
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<div style="width: 40%; float: left;"><br />
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<h3>Progress</h3><br />
<br />
</div><br />
</div><br />
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<div style="width: 97%; float: left;"><br />
<br />
==Delivery Mechanism==<br />
<br />
This work will use the prostate segmentation tools earlier contributed to NAMIC Sandbox: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Queens/ProstateSeg http://viewvc.slicer.org/viewcvs.cgi/trunk/Queens/ProstateSeg]<br />
<br />
==References== <br />
* [[ProstateSegmentationAHM2009 |Prostate segmentation at AHM SLC 2009]]<br />
* [[2009_Summer_project_week_prostate_registration |Prostate registration at Boston 2009 meeting]]<br />
* [[2010_Winter_Project_Week_ProstateSeg |Prostate segmentation at AHM SLC 2010]]<br />
<br />
</div></div>
Fedorov