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mask

Section: User Commands (1)
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NAME

mask - Creates a background mask from a voxel-ordered DW data file by thresholding the average b=0 measurement.

SYNOPSIS

mask [-schemefile <filename> -bgthresh <positive integer>]

DESCRIPTION

Reads a data file from the acquisition scheme specified in the schemefile. Thresholds the average b=0 measurement in each voxel and outputs one or zero indicating whether the average is above the threshold.

EXAMPLES

Create a mask for data file SubjectA.Bfloat:

mask -inputfile SubjectA.Bfloat -schemefile test/A.scheme -bgthresh 200 > SubjectA_M200.char

or, equivalently,

mask -schemefile test/A.scheme -bgthresh 200 < SubjectA.Bfloat> SubjectA_M200.char

OPTIONS

-inputfile <file>: Diffusion-weighted MRI data file in voxel order.
-schemefile <file>: Schemefile.
-bgthresh <integer>: The lower threshold on the average b=0 measurement.
-csfthresh <integer>: The upper threshold on the average b=0 measurement.
-inputdatatype <data type of input>: Specifies the data type of the input file. The data type can be any of the following strings: "char", "short", "int", "long", "float" or "double". See camino(1).
-outputdatatype <data type of output>: Specifies the data type of the output data. The data type can be any of the following strings: "char", "short", "int", "long", "float" or "double". See camino(1).

AUTHORS

Daniel Alexander <camino@cs.ucl.ac.uk>

BUGS

Requires the acquisition to have at least one b=0 measurement. However, you can cheat and create a dummy scheme file with low b measurements set to zero if necessary. Works fine.

This document was created by man2html, using the manual pages.
Time: 02:07:11 GMT, December 04, 2017

Mask