Difference between revisions of "2010 Winter Project Week HARDI CONNECTIVITY"
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<gallery> | <gallery> | ||
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]] | Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]] | ||
| + | Image:ODF_shi_0.png|ODF glyphs | ||
</gallery> | </gallery> | ||
==Key Investigators== | ==Key Investigators== | ||
| − | * UNC-Chapel Hill: Yundi(Wendy) Shi | + | * UNC-Chapel Hill: Deepika Mahalingam, Yundi(Wendy) Shi, Martin Styner |
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<h3>Objective</h3> | <h3>Objective</h3> | ||
| − | We are developing methods to study the connectivity of the developing brain in humans and macaques. The goals for this project week is the development 1) | + | We are developing methods to study the connectivity of the developing brain in humans and macaques. The goals for this project week is the development of 1)a visualization strategy of ODF/HARDI information in Slicer (work with Bloy/Verma/Westin) and 2)a global fiber tractography method using HARDI/ODF information. Long-term goals of the project include application of the tractography results for deformable registration purposes and study of connectivity patterns in brain development. |
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<h3>Approach, Plan</h3> | <h3>Approach, Plan</h3> | ||
| − | * Compare and select the most appropriate higher order diffusion representation for our human and macaque data from early | + | * Compare and select the most appropriate higher order diffusion representation for our human and macaque data from early brain development DWI studies |
| − | * Visualization (development/implementation of modules for Slicer3), in | + | * Visualization (development/implementation of modules for Slicer3), in collaboration with [[2010_Winter_Project_Week_HARDI_RSH | Bloy/Verma/Westin]] |
* Fiber tractography and connectivity information analysis | * Fiber tractography and connectivity information analysis | ||
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<h3>Progress</h3> | <h3>Progress</h3> | ||
| − | We have the matlab implementation of various QBall techniques and have applied those techniques to neonatal human data and primate data. We're also learning to use the CAMINO package and | + | We have the matlab implementation of various QBall techniques and have applied those techniques to neonatal human data and primate data. We're also learning to use the CAMINO package and its use for our purpose. We just started the development for the global fiber tractography. |
| + | |||
| + | *Day 1 - Compile and build HardiRsh([[2010_Winter_Project_Week_HARDI_RSH | Bloy/Verma/Westin]]) with EXECT_OPTION (for ODF calculation) and SLICER_OPTION (for visualization in Slicer3) on a mac os platform | ||
| + | |||
| + | *Day 2 - Trying to build the slicer3 module and use it to load the reconstructed ODF volume and use the binary odf calculation for the primate data. (The data format is in nifti) Meeting with [[ 2010_Winter_Project_Week_Tractography|James Malcolm]] for the possibility of using their fiber tracking technique on our data. | ||
| + | |||
| + | *Day 3 - Apply the ODF calculation implemented by [[2010_Winter_Project_Week_HARDI_RSH | Luke]] to the 1 year old human dataset. | ||
| + | |||
| + | *Day 4 - Learning usage of camino commands to fit multiple tensors to our 1 year old human data and running PASMRI on the same data. Visualize ODF files (nrrd format) in Slicer3 using the module by [[2010_Winter_Project_Week_HARDI_RSH | Luke]] | ||
| + | |||
</div> | </div> | ||
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==References== | ==References== | ||
*P. A. Cook, Y. Bai, S. Nedjati-Gilani, K. K. Seunarine, M. G. Hall, G. J. Parker, D. C. Alexander, Camino: Open-Source Diffusion-MRI Reconstruction and Processing, 14th Scientific Meeting of the International Society for Magnetic Resonance in Medicine, Seattle, WA, USA, p. 2759, May 2006 | *P. A. Cook, Y. Bai, S. Nedjati-Gilani, K. K. Seunarine, M. G. Hall, G. J. Parker, D. C. Alexander, Camino: Open-Source Diffusion-MRI Reconstruction and Processing, 14th Scientific Meeting of the International Society for Magnetic Resonance in Medicine, Seattle, WA, USA, p. 2759, May 2006 | ||
| + | *Fillard et al. A Novel Global Tractography Algorithm Based on an Adaptive Spin Glass Model. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009 pp. 1-8 | ||
</div> | </div> | ||
Latest revision as of 17:40, 8 January 2010
Home < 2010 Winter Project Week HARDI CONNECTIVITY
ODF glyphs
Key Investigators
- UNC-Chapel Hill: Deepika Mahalingam, Yundi(Wendy) Shi, Martin Styner
Objective
We are developing methods to study the connectivity of the developing brain in humans and macaques. The goals for this project week is the development of 1)a visualization strategy of ODF/HARDI information in Slicer (work with Bloy/Verma/Westin) and 2)a global fiber tractography method using HARDI/ODF information. Long-term goals of the project include application of the tractography results for deformable registration purposes and study of connectivity patterns in brain development.
Approach, Plan
- Compare and select the most appropriate higher order diffusion representation for our human and macaque data from early brain development DWI studies
- Visualization (development/implementation of modules for Slicer3), in collaboration with Bloy/Verma/Westin
- Fiber tractography and connectivity information analysis
Progress
We have the matlab implementation of various QBall techniques and have applied those techniques to neonatal human data and primate data. We're also learning to use the CAMINO package and its use for our purpose. We just started the development for the global fiber tractography.
- Day 1 - Compile and build HardiRsh( Bloy/Verma/Westin) with EXECT_OPTION (for ODF calculation) and SLICER_OPTION (for visualization in Slicer3) on a mac os platform
- Day 2 - Trying to build the slicer3 module and use it to load the reconstructed ODF volume and use the binary odf calculation for the primate data. (The data format is in nifti) Meeting with James Malcolm for the possibility of using their fiber tracking technique on our data.
- Day 3 - Apply the ODF calculation implemented by Luke to the 1 year old human dataset.
- Day 4 - Learning usage of camino commands to fit multiple tensors to our 1 year old human data and running PASMRI on the same data. Visualize ODF files (nrrd format) in Slicer3 using the module by Luke
References
- P. A. Cook, Y. Bai, S. Nedjati-Gilani, K. K. Seunarine, M. G. Hall, G. J. Parker, D. C. Alexander, Camino: Open-Source Diffusion-MRI Reconstruction and Processing, 14th Scientific Meeting of the International Society for Magnetic Resonance in Medicine, Seattle, WA, USA, p. 2759, May 2006
- Fillard et al. A Novel Global Tractography Algorithm Based on an Adaptive Spin Glass Model. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009 pp. 1-8
