Algorithm:MGH:New

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Overview of MGH Algorithms

A brief overview of the MGH's algorithms goes here. This should not be much longer than a paragraph. Remember that people visiting your site want to be able to understand very quickly what you're all about and then they want to jump into your site's projects. The projects below are organized into a two column table: the left column is for representative images and the right column is for project overviews. The number of rows corresponds to the number of projects at your site. Put the most interesting and relevant projects at the top of the table. You do not need to organize the table according to subject matter (i.e. do not group all segmentation projects together and all DWI projects together).

MGH Projects

QDEC: An easy to use GUI for group morphometry studies Difficulty: Medium Impact: High Use cases: See Qdec project page Use case: 'Compare the primary eigendirection in two groups to see if they are the same' Difficulty: Low Impact: Medium See: Qdec user page Optimal path calculator (Poistats) Use case: 'Specify 2 points in a diffusion image and tell how connected they are.' Difficulty: High Impact: High Engineering:Project:Non-rigid_EPI_registration Statistical power benefit of ITK nonlinear registration Use case: 'Evaluate benefit of using ITK nonlinear registration for group FA comparisons' Difficulty: Low-Medium Impact: Medium Adding NRRD I/O to Freesurfer Use case: 'Open a NRRD volume in FreeSurfer.' Use case: 'Convert an MGH volume to a NRRD volume with Freesurfer.' Difficulty: Low Impact: Medium Write unit tests for new IO functions (Snyder): in progress Add NrrdIO libraries from Teem to FS source tree, build with autoconf (Snyder): done Write and test FS NRRD IO functions (Snyder, Kindlmann): in progress Develop approriate headers for MGH DWI data (Teich): queued Automate header generation when possible (Teich): queued Spherical Wavelets Cortical Surface Shape Analysis Based on Spherical Wavelets Topology Correction Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops QBALL visualization Use case: 'Visualize q-ball data in Slicer.' Difficulty: Low Impact: Medium Implement ODF polygon decimation algorithm (Tuch) : done Port decimation fileformat into FreeDiffusion Visualizer (Snyder) : done Port QBALL/ODF visualization into Slicer (Estepar/Snyder/Kindlmann/Tuch/Westin): done Implement (Estepar): done Test on mock data set (Estepar): done Demo for real data set (Estepar/Snyder/Kindlmann): done Tensor-based group comparison (Cramer test) Use case: 'Compare DTI images between groups using the full tensor information.' Difficulty: Medium Impact: Medium-High Implement in R (Whitcher/Tuch) : done Power analysis (Whitcher) : done Port to Matlab (Whitcher) : done Validate Matlab version against R (Whitcher) : done Test on group data : done Release bootstrap-only version to test group: done Port FFT method from R to matlab (Whitcher): done Implement FFT method in diffusion development environment (Tuch): done Numerical Recipies Replacement Replacing Numerical Recipes in FreeSurfer (for open sourcing) Use case: 'Unit tests pass with all replacements.' Difficulty: Medium-High Impact: High Write test cases for each algorithm (Snyder, Jen): done Identify replacements (Snyder, Jen): done Integrate required libraries into FreeSurfer build process (Snyder, Jen): done Iteratively replace recipes with substitutes and run tests (Snyder, Jen): done Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms Use Case: 'Atlas-based fully automated whole brain segmentation' Difficulty: Medium-High Impact: Medium-High Implemented in C and distribute with the FreeSurface Package: done