.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH JOINTFUSION "1" "November 2014" "jointfusion 2.1.0~rc2+git3" "User Commands"
.SH NAME
jointfusion \- part of ANTS registration suite
.SH DESCRIPTION
Joint Label Fusion:
usage:
.IP
jointfusion dim mod [options] output_image
.SS "required options:"
.TP
dim
Image dimension (2 or 3)
.TP
mod
Number of modalities or features
.TP
\fB\-g\fR atlas1_mod1.nii atlas1_mod2.nii ...atlasN_mod1.nii atlasN_mod2.nii ...
Warped atlas images
.TP
\fB\-tg\fR target_mod1.nii ... target_modN.nii
Target image(s)
.TP
\fB\-l\fR label1.nii ... labelN.nii
Warped atlas segmentation
.TP
\fB\-m\fR <method> [parameters]
Select voting method. Options: Joint (Joint Label Fusion)
May be followed by optional parameters in brackets, e.g., \fB\-m\fR Joint[0.1,2].
See below for parameters
.SS "other options:"
.TP
\fB\-rp\fR radius
Patch radius for similarity measures, scalar or vector (AxBxC)
Default: 2x2x2
.TP
\fB\-rs\fR radius
Local search radius.
Default: 3x3x3
.TP
\fB\-x\fR label image.nii
Specify an exclusion region for the given label.
.TP
\fB\-p\fR filenamePattern
Save the posterior maps (probability that each voxel belongs to each label) as images.
The number of images saved equals the number of labels.
The filename pattern must be in C printf format, e.g. posterior%04d.nii.gz
.TP
\fB\-w\fR filenamePattern
Save the voting weights as images.
The number of images saved equals the number of atlases.
The filename pattern must be in C printf format, e.g. weight%04d.nii.gz
.TP
\fB\-gp\fR ID_atlas1 ... ID_atlasN
Assign a group ID for each atlas
.TP
\fB\-gpw\fR weight_gp1 ... weight_gpn
Assign the voting weights to each atlas group
.SS "Parameters for -m Joint option:"
.TP
alpha
Regularization term added to matrix Mx for inverse
Default: 0.1
.TP
beta
Exponent for mapping intensity difference to joint error
Default: 2