2010 WinterProject Week MRSIModule - Revision history

Bmenze at 16:12, 8 January 2010

2010-01-08T16:12:10Z

Bmenze: /* Key Investigators */

2010-01-08T16:11:31Z

Key Investigators

Bmenze at 16:00, 8 January 2010

2010-01-08T16:00:27Z

Bmenze at 15:58, 8 January 2010

2010-01-08T15:58:13Z

Bmenze at 15:53, 8 January 2010

2010-01-08T15:53:17Z

Bmenze: /* Key Investigators */

2010-01-08T15:27:36Z

Key Investigators

Bmenze: /* Key Investigators */

2010-01-08T15:26:50Z

Key Investigators

Bmenze: Created page with 'NOTOC Image:PW-SLC2010.png|Projects List Image:Mrsi parametric-map-NAA 3d.jpg|MRSI metabolite maps visualized in Slicer Image:…'

2009-12-10T17:56:23Z

Created page with '__NOTOC__ <gallery> Image:PW-SLC2010.png|Projects List Image:Mrsi parametric-map-NAA 3d.jpg|MRSI metabolite maps visualized in Slicer Image:…'

New page

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
Image:Mrsi parametric-map-NAA 3d.jpg|MRSI metabolite maps visualized in Slicer
Image:Spectral fitting mrs.png|Fitting metabolite models to the MRS signal of tumorous brain tissue (top: baseline removal; bottom: resonance line model fits)
</gallery>

==Key Investigators==
* MIT: Bjoern Menze, Polina Golland

<div style="margin: 20px;">

<div style="width: 32%; float: left; padding-right: 3%;">
<h3>Objective</h3>
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.

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.
</div>

<div style="width: 32%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
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. Current fitting routines require, however, several external software libraries not to be distributed, installed and used easily.

We want to replace these libraries by using standard optimization routines from Python being available in Slicer.
</div>

<div style="width: 30%; float: left;">
<h3>Progress</h3>
</div>

@@ Line 33: / Line 33: @@
 * We adapted the current MRSI processing routine to be separable into several sub-routines, each of which to be usable as external CLI module and depending on few (or single) external libraries only.
-* We worked towards integrating an exemplary subroutine -- together with its external library -- as an external CLI module, and potentially to be distributed as a Slicer Extension.
+* We worked towards integrating an exemplary subroutine -- together with its external library -- as an external CLI module, potentially to be distributed as a Slicer Extension.
 Separate subroutines can be integrated using a Slicer Wizard in accordance with the signal processing workflow (see ''Results'' figure above).
 </div>

@@ Line 4: / Line 4: @@
 Image:Mrsi parametric-map-NAA 3d.jpg|MRSI metabolite maps visualized in Slicer
 Image:Spectral fitting mrs.png|Fitting metabolite models to the MRS signal of tumorous brain tissue (top: baseline removal; bottom: resonance line model fits)
-Image:Workflow_MRSI_signal_processing.png| Workflow for the MRSI signal processing. Each processing step is to be realized as an individual external module.
+Image:Workflow_MRSI_signal_processing.png| ''Results'': Workflow for the MRSI signal processing. Each processing step is to be realized as an individual external module.
 </gallery>
@@ Line 35: / Line 35: @@
 * We worked towards integrating an exemplary subroutine -- together with its external library -- as an external CLI module, and potentially to be distributed as a Slicer Extension.
-Separate subroutines can be integrated using a Slicer Wizard in accordance with the signal processing workflow (see Figure above).
+Separate subroutines can be integrated using a Slicer Wizard in accordance with the signal processing workflow (see ''Results'' figure above).
 </div>

@@ Line 28: / Line 28: @@
 <div style="width: 30%; float: left;">
 <h3>Progress</h3>
-We adapted the current MRSI processing routine to be separable into several sub-routines (see Figure), each of which to be usable as external CLI module and depending on few (or single) external libraries only.
+* We adapted the current MRSI processing routine to be separable into several sub-routines, each of which to be usable as external CLI module and depending on few (or single) external libraries only.
-We worked towards integrating an exemplary subroutine -- together with its external library -- as an external CLI module, and potentially to be distributed as a Slicer extension.
+* We worked towards integrating an exemplary subroutine -- together with its external library -- as an external CLI module, and potentially to be distributed as a Slicer Extension.
 </div>

@@ Line 31: / Line 31: @@
 We adapted the current MRSI processing routine to be separable into several sub-routines (see Figure), each of which to be usable as external CLI module and depending on few (or single) external libraries only.
-We worked towards integrating an exemplary subroutine -- together with its external library -- as an external CLI module into Slicer potentially to be distributed as a Slicer extension.
+We worked towards integrating an exemplary subroutine -- together with its external library -- as an external CLI module, and potentially to be distributed as a Slicer extension.
 </div>

@@ Line 4: / Line 4: @@
 Image:Mrsi parametric-map-NAA 3d.jpg|MRSI metabolite maps visualized in Slicer
 Image:Spectral fitting mrs.png|Fitting metabolite models to the MRS signal of tumorous brain tissue (top: baseline removal; bottom: resonance line model fits)
 </gallery>
@@ Line 12: / Line 13: @@
 <div style="margin: 20px;">
-<div style="width: 32%; float: left; padding-right: 3%;">
+<div style="width: 30%; float: left; padding-right: 2%;">
 <h3>Objective</h3>
 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.
@@ Line 19: / Line 20: @@
 </div>
-<div style="width: 32%; float: left; padding-right: 3%;">
+<div style="width: 30%; float: left; padding-right: 2%;">
 <h3>Approach, Plan</h3>
 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. Current fitting routines require, however, several external software libraries not to be distributed, installed and used easily.
@@ Line 26: / Line 27: @@
 </div>
-<div style="width: 30%; float: left;">
+<div style="width: 35%; float: left;">
 <h3>Progress</h3>
 We focused on the second option and investigated directions for using third party libraries from within Slicer.

2010 WinterProject Week MRSIModule - Revision history

Bmenze at 16:12, 8 January 2010

Bmenze: /* Key Investigators */

Bmenze at 16:00, 8 January 2010

Bmenze at 15:58, 8 January 2010

Bmenze at 15:53, 8 January 2010

Bmenze: /* Key Investigators */

Bmenze: /* Key Investigators */

Bmenze: Created page with '__NOTOC__ Image:PW-SLC2010.png|Projects List Image:Mrsi parametric-map-NAA 3d.jpg|MRSI metabolite maps visualized in Slicer Image:…'

Bmenze: Created page with 'NOTOC Image:PW-SLC2010.png|Projects List Image:Mrsi parametric-map-NAA 3d.jpg|MRSI metabolite maps visualized in Slicer Image:…'