NAMIC Wiki - User contributions [en]

2011 Winter Project Week:MRSI module and SIVIC interface

2011-01-14T07:42:19Z

Jasonc: added image

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:Spectral fitting mrs.png|Figure 1 - Fitting metabolite models to the MRS signal of tumorous brain tissue.
Image:Mrsi parametric-map-NAA 3d.jpg|Figure 2 - MRSI metabolite maps visualized in Slicer
Image:Mrsi_slicer_sivic.jpg| Figure 3 - Screenshot of the SIVIC MRSI module integrated into Slicer.
Image:Sivic_slicer_slc_mets.jpg| Figure 4 - MRSI metabolite maps generated in SIVIC module referenced to anatomical (FLAIR) image.
</gallery>

==Key Investigators==
* MIT: Bjoern Menze, Mangpo Phothilimthana, Polina Golland
* UCSF: Olson Beck, Jason Crane, Sarah Nelson ([http://www.radiology.ucsf.edu/nelsonlab/ Nelson Lab])

==Project==
<div style="margin: 10px;">

<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.

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: 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.

We want to integrate the [http://wiki.na-mic.org/Wiki/index.php/2010_WinterProject_Week_MRSIModule currently] available MRSI quantitation routines with the [http://sourceforge.net/apps/trac/sivic/ SIVIC] Slicer interface developed at the UCSF.
More specifically we want to integrate the previously developed signal processing routines (Fig. 1) into the svk library of the SIVIC framework, and realize the joint display of metabolic maps (Fig. 2) and spectral information (Fig. 3) within the current prototype of the Slicer module.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
</div>

</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify) YES: part of the 'vtk style' svk library of the SIVIC framework

==References==
* Jason C. Crane, Marram P. Olson, Sarah J. Nelson. SIVIC: An Extensible Open-Source DICOM MR Spectroscopy Software Framework and Application Suite. Proc ISMRM 2010. 3354.

</div>

File:Sivic slicer slc mets.jpg

2011-01-14T07:40:44Z

Jasonc: metabolite maps from SIVIC module

metabolite maps from SIVIC module

File:Sivic slicer slc2.tif

2011-01-14T07:35:47Z

Jasonc: uploaded a new version of "File:Sivic slicer slc2.tif"

multiple metabolite maps generated from MRS data on anatomical image

2011 Winter Project Week:MRSI module and SIVIC interface

2011-01-14T07:06:20Z

Jasonc: added met maps

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:Spectral fitting mrs.png|Figure 1 - Fitting metabolite models to the MRS signal of tumorous brain tissue.
Image:Mrsi parametric-map-NAA 3d.jpg|Figure 2 - MRSI metabolite maps visualized in Slicer
Image:Mrsi_slicer_sivic.jpg| Figure 3 - Screenshot of the SIVIC MRSI module integrated into Slicer.
Image:Sivic_slicer_slc2.tif| Figure 4 - MRSI metabolite maps generated in SIVIC module referenced to anatomical (FLAIR) image.
</gallery>

==Key Investigators==
* MIT: Bjoern Menze, Mangpo Phothilimthana, Polina Golland
* UCSF: Olson Beck, Jason Crane, Sarah Nelson ([http://www.radiology.ucsf.edu/nelsonlab/ Nelson Lab])

==Project==
<div style="margin: 10px;">

<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.

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: 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.

We want to integrate the [http://wiki.na-mic.org/Wiki/index.php/2010_WinterProject_Week_MRSIModule currently] available MRSI quantitation routines with the [http://sourceforge.net/apps/trac/sivic/ SIVIC] Slicer interface developed at the UCSF.
More specifically we want to integrate the previously developed signal processing routines (Fig. 1) into the svk library of the SIVIC framework, and realize the joint display of metabolic maps (Fig. 2) and spectral information (Fig. 3) within the current prototype of the Slicer module.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
</div>

</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify) YES: part of the 'vtk style' svk library of the SIVIC framework

==References==
* Jason C. Crane, Marram P. Olson, Sarah J. Nelson. SIVIC: An Extensible Open-Source DICOM MR Spectroscopy Software Framework and Application Suite. Proc ISMRM 2010. 3354.

</div>

File:Sivic slicer slc2.tif

2011-01-14T07:02:40Z

Jasonc: multiple metabolite maps generated from MRS data on anatomical image

multiple metabolite maps generated from MRS data on anatomical image

2011 Winter Project Week:MRSI module and SIVIC interface

2011-01-06T19:00:57Z

Jasonc: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
Image:Spectral fitting mrs.png|Figure 1 - Fitting metabolite models to the MRS signal of tumorous brain tissue.
Image:Mrsi parametric-map-NAA 3d.jpg|Figure 2 - MRSI metabolite maps visualized in Slicer
Image:Mrsi_slicer_sivic.jpg| Figure 3 - Screenshot of the SIVIC MRSI module integrated into Slicer.
</gallery>

==Key Investigators==
* MIT: Bjoern Menze, Mangpo Phothilimthana, Polina Golland
* UCSF: Olson Beck, Jason Crane, Sarah Nelson ([http://www.radiology.ucsf.edu/nelsonlab/ Nelson Lab])

==Project==
<div style="margin: 10px;">

<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.

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: 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.

We want to integrate the [http://wiki.na-mic.org/Wiki/index.php/2010_WinterProject_Week_MRSIModule currently] available MRSI quantitation routines with the [http://sourceforge.net/apps/trac/sivic/ SIVIC] Slicer interface developed at the UCSF.
More specifically we want to integrate the previously developed signal processing routines (Fig. 1) into the svk library of the SIVIC framework, and realize the joint display of metabolic maps (Fig. 2) and spectral information (Fig. 3) within the current prototype of the Slicer module.
</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>
</div>

</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify) YES: part of the 'vtk style' svk library of the SIVIC framework

==References==
* Jason C. Crane, Marram P. Olson, Sarah J. Nelson. SIVIC: An Extensible Open-Source DICOM MR Spectroscopy Software Framework and Application Suite. Proc ISMRM 2010. 3354.

</div>