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targetprobs2txt

Section: User Commands (1)
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NAME

targetprobs2txt - Converts results of connectivity based segmentation to a text file.

SYNOPSIS

targetprobs2txt -inputroot <root> -seedfile <file> -targetfile <file> -pd <pd> -regionindex <index> -outputfile <file>

DESCRIPTION

This tool reads PICo connection probability maps, seeds and an associated target file, and outputs a table of the seed points and the connection probabilities to each target region. The output format is

x y z cp_1 cp_2 ... cp_n
x y z cp_1 cp_2 ... cp_n

Where x,y,z are the voxel coordinates of the seed point, and there are n targets in the target file. The target regions are numbered in ascending order according to their intensity value in the target file.

EXAMPLES

Pass streamlines from the file tracts.Bfloat to procstreamlines, to produce target connection probability images.

cat tracts.Bfloat | procstreamlines -seedfile seeds.hdr -targetfile targets.hdr -outputcp -outputroot subject_targetcp_

The seed file contains two ROIs labelled 1, with m seeds, and 2, with n seeds. The file tracts.Bfloat contains streamlines tracked over the both ROIs with track. Each seed point contains one principal direction.

The above command produces the files

subject_targetcp_1_[1,2,...,m].[ext]
subject_targetcp_2_[1,2,...,n].[ext]

We get the target probabilities of these files with

targetprobs2txt -seedfile seeds.hdr -targetfile targets.hdr -inputroot subject_targetcp_ -regionindex 1 > targetprobs_r1.txt

targetprobs2txt -seedfile seeds.hdr -targetfile targets.hdr -inputroot subject_targetcp_ -regionindex 2 > targetprobs_r2.txt

OPTIONS

-inputroot <root>

Root of the connection probability images. This is the path to the files up to (but not including) the region index.

-seedfile <file>

The seed file used for the tracking.

-targetfile <file>

The target image.

-pd <pd>

Index of the principal direction followed at the seed point. Default is 1.

-regionindex <index>

Index of the ROI in the seed file. Default is 1.

AUTHORS

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

BUGS

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

Targetprobs2txt