https://www.na-mic.org/w/index.php?action=history&feed=atom&title=2009_Summer_Project_Week_MRSI-Module
2009 Summer Project Week MRSI-Module - Revision history
2026-04-05T18:29:33Z
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Bmenze at 14:49, 25 June 2009
2009-06-25T14:49:03Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 14:49, 25 June 2009</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 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 style="font-weight: bold; text-decoration: none;">We adapted the signal processing module to the 3T image data of the UIowa phantom data.</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 style="font-weight: bold; text-decoration: none;"></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 style="font-weight: bold; text-decoration: none;">We verified the registration of the spectroscopic images, now allowing to jointly visualize parametric maps (i.e., metabolic maps) of the MRSI signal processing module together with morphological images in Slicer (see Figure 1 below).</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 style="font-weight: bold; text-decoration: none;"></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 style="font-weight: bold; text-decoration: none;">We defined an interface between the MRSI signal processing and the BrainCSI visualization module -- based on structured grids and later to be used in the 3DSlicer.</ins></div></td></tr>
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<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 style="font-weight: bold; text-decoration: none;">[[File:Mrsi parametric-map-NAA 3d.jpg|thumpnail|750px]]</ins></div></td></tr>
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<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 style="font-weight: bold; text-decoration: none;">Figure 1 - 3D parametric map showing the NAA amplitudes of the spectra in a MR spectroscopic image in Slicer.</ins></div></td></tr>
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Bmenze
https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week_MRSI-Module&diff=39117&oldid=prev
Tkapur at 02:31, 22 June 2009
2009-06-22T02:31:50Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 02:31, 22 June 2009</td>
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<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:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]</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:PW2009-v3.png|[[2009_Summer_Project_Week<ins class="diffchange diffchange-inline">#Projects</ins>|Project Week Main Page]]</div></td></tr>
<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:Mrsi slicer.jpg|Color-coded MRSI in the localization and grading of brain tumors</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:Mrsi slicer.jpg|Color-coded MRSI in the localization and grading of brain tumors</div></td></tr>
<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:Spectral fitting mrs.png|Fitting metabolite models to the MRS signal of tumorous brain tissue (top: baseline removal; bottom: resonance line model fits)</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:Spectral fitting mrs.png|Fitting metabolite models to the MRS signal of tumorous brain tissue (top: baseline removal; bottom: resonance line model fits)</div></td></tr>
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Tkapur
https://www.na-mic.org/w/index.php?title=2009_Summer_Project_Week_MRSI-Module&diff=37934&oldid=prev
Bmenze: Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:Mrsi slicer.jpg|Color-coded MRSI in the localization and grading of brain tumors...'
2009-06-01T18:46:23Z
<p>Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|<a href="/wiki/2009_Summer_Project_Week" title="2009 Summer Project Week">Project Week Main Page</a> Image:Mrsi slicer.jpg|Color-coded MRSI in the localization and grading of brain tumors...'</p>
<p><b>New page</b></p><div>__NOTOC__<br />
<gallery><br />
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]<br />
Image:Mrsi slicer.jpg|Color-coded MRSI in the localization and grading of brain tumors<br />
Image:Spectral fitting mrs.png|Fitting metabolite models to the MRS signal of tumorous brain tissue (top: baseline removal; bottom: resonance line model fits)<br />
</gallery><br />
<br />
==Key Investigators==<br />
* MIT: Bjoern Menze, Polina Golland<br />
* Iowa: Jeff Yager, Vince Magnotta<br />
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<h3>Objective</h3><br />
Magnetic resonance spectroscopic imaging (MRSI) is a non-invasive diagnostic method used to determine the relative abundance of specific metabolites at arbitrary locations in vivo. Certain diseases -- such as tumors in brain, breast and prostate -- can be can be associated with characteristic changes in the metabolic level. <br />
<br />
The objective of the current project is to develop a module proving the means for the processing and visualization of MRSI -- and thus for a joint analysis of magnetic resonance spectroscopic images together with other imaging modalities -- in Slicer.<br />
</div><br />
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<h3>Approach, Plan</h3><br />
Spectral fitting routines have been implemented, using a HSVD filter for water peak removal and baseline estimation, and a constrained non-linear least squares optimization for the fit of the resonance line models. MRSI post-processing routines for partial volume correction are available from the [http://www.nitrc.org/projects/braincsi BrainCSI] toolbox. <br />
<br />
Our plan for the project week is to first integrate the spectral fitting routines into a Slicer module and to validate this module using MRSI phantom data. We then want to work towards interfacing signal processing module and post-processing tools.<br />
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<h3>Progress</h3><br />
</div></div>
Bmenze