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

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QDEC: An easy to use GUI for group morphometry studies

  • Use case: 'Compare the primary eigendirection in two groups to see if they are the same'
  • Difficulty: Low
  • Impact: Medium

See: Qdec user page

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Optimal path calculator (Poistats)

  • Use case: 'Specify 2 points in a diffusion image and tell how connected they are.'
  • Difficulty: High
  • Impact: High
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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
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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
  1. Write unit tests for new IO functions (Snyder): in progress
  2. Add NrrdIO libraries from Teem to FS source tree, build with autoconf (Snyder): done
  3. Write and test FS NRRD IO functions (Snyder, Kindlmann): in progress
  4. Develop approriate headers for MGH DWI data (Teich): queued
  5. Automate header generation when possible (Teich): queued
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Spherical Wavelets

Cortical Surface Shape Analysis Based on Spherical Wavelets

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Topology Correction

Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops


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QBall Visualization

  • Use case: 'Visualize q-ball data in Slicer.'
  • Difficulty: Low
  • Impact: Medium
  1. Implement ODF polygon decimation algorithm (Tuch) : done
  2. Port decimation fileformat into FreeDiffusion Visualizer (Snyder) : done
  3. Port QBALL/ODF visualization into Slicer (Estepar/Snyder/Kindlmann/Tuch/Westin): done
    1. Implement (Estepar): done
    2. Test on mock data set (Estepar): done
    3. Demo for real data set (Estepar/Snyder/Kindlmann): done
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Tensor-based group comparison (Cramer test)

  • Use case: 'Compare DTI images between groups using the full tensor information.'
  • Difficulty: Medium
  • Impact: Medium-High
  1. Implement in R (Whitcher/Tuch) : done
  2. Power analysis (Whitcher) : done
  3. Port to Matlab (Whitcher) : done
  4. Validate Matlab version against R (Whitcher) : done
  5. Test on group data : done
  6. Release bootstrap-only version to test group: done
  7. Port FFT method from R to matlab (Whitcher): done
  8. Implement FFT method in diffusion development environment (Tuch): done
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Numerical Recipies Replacement

Replacing Numerical Recipes in FreeSurfer (for open sourcing)

  • Use case: 'Unit tests pass with all replacements.'
  • Difficulty: Medium-High
  • Impact: High
  1. Write test cases for each algorithm (Snyder, Jen): done
  2. Identify replacements (Snyder, Jen): done
  3. Integrate required libraries into FreeSurfer build process (Snyder, Jen): done
  4. Iteratively replace recipes with substitutes and run tests (Snyder, Jen): done
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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
  1. Implemented in C and distribute with the FreeSurface Package: done