Diffusion MRI Design Notes

This page is a work in progress.

• Win's Pipeline - In project/brain/pipeline/coro/ and install_linux/bin/brain/

coro_dicom2niifti.py - Convert Dicom files to Niifti format.
coro_register.py     - Coregister a set of MRI images against a reference template image.
                       Produce registered niifti DWIs for performing dti steps.
coro_dti.py          - Compute a dti; the CIT pipelne does a better job.

• Legacy Pipeline - In project/brain/pipeline/ and install_linux/bin/brain/

format_conversion/   niftii2mriimage - Convert a registered niifti DWI to Mri Image format.
tensor/mritensorop/  mritensor       - Convert an Mri Image to a DTI and scalar images.
streamtube/tubegen/  tubegen         - Convert a DTI to a DTI tractogram.

tubefa???
project/brain/brainapp               - Interactively create statistics.

• DTK Pipeline tools - In import/dtk/dtk_v0.5_linux/ and import/dtk/trackvis_v0.5_linux/

DTK - Convert DWIs to either a DTI or QBI.
      The CIT pipeline does a better job.
DTK - Convert a DTI or QBI to a tractogram
TrackVis - Convert a tractogram or QBI to statistics.

• New Pipeline in the Works