open source, neuro, learning, collaboration, sound theory, solid results

Software

ITK: core image processing and SimpleITK.

Image Registration – Advanced Normalization Tools (ANTs) SyN.  Compile ANTs.

Image Segmentation – Atropos program (via ANTs).   Link to paper.   Also Paul Yushkevich’s ITK-SNAP!

Bias Correction –  N4 (via ANTs).

Paraview and mricron are useful for visualization.

Other useful tools:

InSANE surface-based visualization and mapping.  Compile with these instructions.

Sparse canonical correlation analysis for neuroimaging (SCCAN): Email for info.  paper.

Topologically constrained segmentation (via ANTs, git version).

Pipedream depends on ANTs and Camino. A processing pipeline for neuroimaging software: T1, DTI, ASL/CBF and (in development) fMRI. Its longitudinal component was used here.

Here is an evaluation of ANTs affine registration against FSL affine registration: Pretty similar.  An in-depth evaluation of ANTs is herehere and here.

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