NAMIC Wiki - User contributions [en]

T1 mapping for variable flip angle

2015-01-10T22:17:06Z

Artmnv: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:T1_Mapping_Module_Results.jpg | T1 Mapping UI and Result using MGH Brain Tumor MR
</gallery>

==Key Investigators==

* MGH: Xiao Da, Artem Mamonov, Jayashree Kalpathy-Cramer
* BWH: Andriy Fedorov

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Estimate effective T1 from multi-spectral FLASH MRI scans with different flip angles
* Implement T1 mapping algorithm as a Slicer extension.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a Slicer module for T1 mapping for multiple flip angles using Python script
* Run Python script and [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ms_fitparms Freesurfer code] on [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* Test the Slicer module on MGH Brain Tumor MR Data with multiple flip angles
* Go through Slicer tutorials and developer forum to learn how to implement Slicer extensions.
* Go over VTK documentation to learn how it works.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Compared the results using Python with Freesurfer and ground truth of T1 for QIBA data
* T1 mapping results on QIBA data using Slicer+Python are almost identical to the results using Freesurfer and comparable with the ground truth.
* Implemented T1 mapping as a Slicer extension using python. The extension has GUI that as an input takes six DICOM images with corresponding flip angles and repetition time. The extension computes T1s and stores them in a new VTK volume node.
</div>
</div>

==References==

* [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* [http://europepmc.org/articles/pmc3620726 Basic equation for T1]
* [http://slicer-devel.65872.n3.nabble.com/VTK-volume-from-numpy-Array-VTK-volume-td4033216.html how to create a new vtk volume node]
* [http://www.vtk.org/Wiki/index.php?title=VTK/Examples/Python/vtkWithNumpy&oldid=37957 numpy array in vtk]

T1 mapping for variable flip angle

2015-01-10T22:16:32Z

Artmnv: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:T1_Mapping_Module_Results.jpg | T1 Mapping UI and Result using MGH Brain Tumor MR
</gallery>

==Key Investigators==

* MGH: Xiao Da, Artem Mamonov, Jayashree Kalpathy-Cramer
* BWH: Andriy Fedorov

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Estimate effective T1 from multi-spectral FLASH MRI scans with different flip angles
* Implement T1 mapping algorithm as a Slicer extension.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a Slicer module for T1 mapping for multiple flip angles using Python script
* Run Python script and [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ms_fitparms Freesurfer code] on [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* Test the Slicer module on MGH Brain Tumor MR Data with multiple flip angles
* Go through Slicer tutorials and developer forum to learn how to implement Slicer extensions.
* Go over VTK documentation to learn how it works.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Compared the results using Python with Freesurfer and ground truth of T1 for QIBA data
* T1 mapping results on QIBA data using Slicer+Python are almost identical to the results using Freesurfer and comparable with the ground truth.
* Implemented T1 mapping as a Slicer extension using python. The extension has GUI that as an input takes 6 DICOM images with corresponding flip angles and repetition time. The extension computes T1s and stores them in a new VTK volume node.
</div>
</div>

==References==

* [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* [http://europepmc.org/articles/pmc3620726 Basic equation for T1]
* [http://slicer-devel.65872.n3.nabble.com/VTK-volume-from-numpy-Array-VTK-volume-td4033216.html how to create a new vtk volume node]
* [http://www.vtk.org/Wiki/index.php?title=VTK/Examples/Python/vtkWithNumpy&oldid=37957 numpy array in vtk]

T1 mapping for variable flip angle

2015-01-09T18:05:30Z

Artmnv: /* References */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:T1_Mapping_Module_Results.jpg | T1 Mapping UI and Result using MGH Brain Tumor MR
</gallery>

==Key Investigators==

* MGH: Xiao Da, Artem Mamonov, Jayashree Kalpathy-Cramer
* BWH: Andriy Fedorov

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Estimate effective T1 from multi-spectral FLASH MRI scans with different flip angles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Create a Slicer module for T1 mapping for multiple flip angles using Python script
* Run Python script and [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ms_fitparms Freesurfer code] on [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* Test the Slicer module on MGH Brain Tumor MR Data with multiple flip angles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Compared the results using Python with Freesurfer and ground truth of T1 for QIBA data
* T1 mapping results on QIBA data using Slicer+Python are almost identical to the results using Freesurfer and comparable with the ground truth
</div>
</div>

==References==

* [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* [http://europepmc.org/articles/pmc3620726 Basic equation for T1]
* [http://slicer-devel.65872.n3.nabble.com/VTK-volume-from-numpy-Array-VTK-volume-td4033216.html how to create a new vtk volume node]
* [http://www.vtk.org/Wiki/index.php?title=VTK/Examples/Python/vtkWithNumpy&oldid=37957 numpy array in vtk]

T1 mapping for variable flip angle

2015-01-05T03:39:57Z

Artmnv: /* References */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:T1_Mapping_Slicer.png | T1 Mapping UI build with Python
</gallery>

==Key Investigators==

* MGH: Xiao Da, Artem Mamonov, Jayashree Kalpathy-Cramer
* BWH: Andriy Fedorov

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Estimate effective T1 from multi-spectral FLASH MRI scans with different flip angles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Creating a Slicer module for T1 mapping for multiple flip angles using Python script
* Running Python script and [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ms_fitparms Freesurfer code] on [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Comparing the results using Python with Freesurfer and ground truth of T1
</div>
</div>

==References==

* [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* [http://europepmc.org/articles/pmc3620726 Basic equation for T1]