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subsetscheme

Section: User Commands (1)
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NAME

subsetscheme - Create scheme files from a subset of directions in an existing scheme

SYNOPSIS

subsetscheme -schemefile <file> -subsetpoints <points> -outputroot <root> [-imagelist <list>]

DESCRIPTION

This program takes the output of subsetpoints and produces scheme files corresponding to the subsets. Each subset scheme file contains ALL the unweighted (q=0) measurements in the original scheme, as well as all measurements along the gradient directions in the subset.

OUTPUT

Subset scheme files - the measurements in the original scheme that correspond to the gradient directions in the subsetpoints file are output as outputRoot_[0...N-1].scheme, where there are N subsets.

Subset indices - the integer indices of the measurements from the full scheme that are in the subset, indexed from zero.

Image lists - If an image list is provided with the -imagelist option, the subset image lists are produced. The image list should be one line per measurement, containing the file name of the associated image volume. This can be produced from a 4D Nifti image with split4dnii.

EXAMPLES

Begin with an existing scheme file, A.scheme, which consists of 3 b=0 measurements and 60 b=1000 s / mm^2 measurements spread over the sphere. The 60 diffusion-weighted measurements are stored in the file A.points.

subsetpoints -inputfile A.points -pointspersubset 20 20 20 -outputfile A_subsets

Create scheme files for each of the subsets

subsetscheme -schemefile A.scheme -subsetpoints A_subsets -outputroot subset

The files subset_[0,1,2].scheme are created, each containing the 3 b=0 measurements, followed by the b=1000 measurements in each subset.

If the diffusion-weighted images are stored as Nifti volumes, an image list can also be created for the subsets. If all 63 volumes are listed in the file imagelist.txt, then the command

subsetscheme -schemefile A.scheme -subsetpoints A_subsets -outputroot subset -imagelist imagelist.txt

will also produce subset_[0,1,2].imagelist, which contains the volumes in each subset.

OPTIONS

-schemefile: Scheme file for the complete imaging scheme.
-subsetpoints: Output from subsetpoints containing one or more subsets of the directions in the scheme file.
-outputroot: Root for the output file names.
-imagelist: Image list containing file names of raw DWI images for the complete imaging scheme. These will be parsed and an image list will be created for each subset.

AUTHORS

Philip Cook <camino@cs.ucl.ac.uk>

BUGS

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Time: 02:07:11 GMT, December 04, 2017

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