CINCH 1.0 BETA
Precomputation parameters for DTI-Query/CINCH
The preprocessing steps and motivation are described in detail in our paper.
This document just serves as an overview or summary of the steps
necessary to prepare the DTI data for the DTI-Query software. One
can either run a GUI version of the precomputation
(dtiprecompute_gui) or a command line version of the software
(dtiprecompute_cmd). Either version of the software allows the user
the same control over precomputation.
- Tensors file - This is the tensor coefficients file as
in the data
format section. This is the only required input to the
precomputation. Note that you are responsible for converting your own DTI
data to the NIFTI format. One way to do this is to use the AFNI image
processing tools - See here for details.
- Order of tensor components - specify the order in which tensor
components appear in the input file.
- Output directory - specify the directory where output files (paths an FA image) will be placed.
- Output prefix - output files will be named [prefix]_fa.nii.gz and [prefix]_pathways.pdb.
- Brain mask file (optional) - This file can be used to limit
voxels of the mask that have a value greater than 0.
- Path Step Size - Controls how short each step is
pathway computation (in millimeters).
- Space Between Seed Points - Sets the spacing (in
millimeters) between each seed point, per dimension. This indirectly
controls the number of pathways that will get created, since each seed
point is the beginning of a pathway. Note that paths will only be
created if the seed point passes the FA and mask tests.
- FA Termination Threshold - Stops pathway
generation in voxels with low Fractional Anisotropy
- Angle Termination Threshold - Stops pathway
the next path step produces a critical bend in the pathway.
- Min/Max Pathway Length - Sets the minimum or maximum pathway length
to be included. Pathways that fall outside the range are discarded.
- Precompute STT/TEND paths - Save some time in precomputation if you are not interested in using a particular algorithm.
- Numerical Integration Method (for STT) - Specifies the integration
method used for the STT path tracing algorithm. Options include Euler's
method, Runge Kutta 2nd order, or Runge Kutta 4th order.
Questions? Problems? E-mail