AnalyzingDiffusion - MRC CBU Imaging Wiki

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Principles of Diffusion MRI

Here you can find a brief summary of the physical principles behind acquisition and analysis of diffusion-wieghted MRI images. attachment:Diffusion_and_MRI.pdf

Sequences for Diffusion

On the 4th of December 2009 there was a meeting held at the Unit to discuss the new CBU standard protocol for acquisition of diffusion weighted images ([:MriPhysicsAndAnalysisForCognitiveNeuroscientists:MR physics & analysis for cognitive neuroscientists]).

Here you can find some generic guidelines for chosing the voxel size/shape for you diffusion MRI experiment. attachment:Diffuson_voxel_size.doc

The new standard CBU DTI sequence acquires isotopic voxels with dimensions 2x2x2mm3. The gaps between slices have also been removed, and instead we use interleaved slice acquisition to avoid crosstalk artefacts (more information here attachment:Desc_vs_Int.doc ).

Analyzing diffusion data

For the moment we are using FSL

See SiemensDiffusionImages for an explanation of the images that the Siemens Trio writes out from a diffusion run.

Here are some notes on getting going with the fdt package for diffusion analysis in FSL: DiffusionFdtNotes

We had in informal meeting to share experience between the WBIC, FSL, and CSL: DiffusionMeeting10May2007