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Man: Mask

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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>

 

SEE ALSO

trd(1), dtpds(1), dtfit(1), twotenfit(1), threetenfit(1), modelfit(1).

 

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.

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Index

NAME

SYNOPSIS

DESCRIPTION

EXAMPLES

OPTIONS

AUTHORS

SEE ALSO

BUGS

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