.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH CREATETILEDMOSAIC "1" "September 2017" "CreateTiledMosaic 2.1.0" "User Commands"
.SH NAME
CreateTiledMosaic \- part of ANTS registration suite
.SH DESCRIPTION
.SS "COMMAND:"
.IP
CreateTiledMosaic
.IP
Render a 3\-D image volume with optional Rgb overlay.
.SS "OPTIONS:"
.HP
\fB\-i\fR, \fB\-\-input\-image\fR inputImageFilename
.IP
Main input is a 3\-D grayscale image.
.HP
\fB\-r\fR, \fB\-\-rgb\-image\fR rgbImageFilename
.IP
An optional Rgb image can be added as an overlay. It must have the same image
geometry as the input grayscale image.
.HP
\fB\-x\fR, \fB\-\-mask\-image\fR maskImageFilename
.IP
Specifies the ROI of the RGB voxels used.
.HP
\fB\-a\fR, \fB\-\-alpha\fR value
.IP
If an Rgb image is provided, render the overlay using the specified alpha
parameter.
.HP
\fB\-o\fR, \fB\-\-output\fR tiledMosaicImage
.IP
The output consists of the tiled mosaic image.
.HP
\fB\-t\fR, \fB\-\-tile\-geometry\fR RxC
.IP
The tile geometry specifies the number of rows and columns in the output image.
For example, if the user specifies '5x10', then 5 rows by 10 columns of slices
are rendered. If R < 0 and C > 0 (or vice versa), the negative value is selected
based on direction.
.HP
\fB\-d\fR, \fB\-\-direction\fR 0/1/2
.IP
Specifies the direction of the slices. If no direction is specified, the
direction with the coarsest spacing is chosen.
.TP
\fB\-p\fR, \fB\-\-pad\-or\-crop\fR padVoxelWidth
[padVoxelWidth,<constantValue=0>]
[lowerPadding[0]xlowerPadding[1],upperPadding[0]xupperPadding[1],constantValue]
.IP
The user can specify whether to pad or crop a specified voxel\-width boundary of
each individual slice. For this program, cropping is simply padding with
negative voxel\-widths. If one pads (+), the user can also specify a constant pad
value (default = 0). If a mask is specified, the user can use the mask to define
the region, by using the keyword "mask" plus an offset, e.g. "\-p mask+3".
.HP
\fB\-s\fR, \fB\-\-slices\fR Slice1xSlice2xSlice3...
.IP
numberOfSlicesToIncrement
[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]
.IP
This option gives the user more control over what slices to use for rendering.
The user can specify specific slices for a particular order. Alternatively the
user can specify the number slices to increment with the optional specification
of which slices to start and end the sequence. A negative value for the
numberOfSlicesToIncrement causes rendering in the reverse order. For the third
option, minSlice < maxSlice. If a mask is specified, the user can use the mask
to define the region, by using the keyword "mask" plus an offset, e.g. "\-s
[1,mask\-3,200]".For the third option, minSlice < maxSlice.
.HP
\fB\-f\fR, \fB\-\-flip\-slice\fR flipXxflipY
.IP
Flip individual slice images horizontally and/or vertically, specified e.g. as
\&'0x1' or '1x1'.
.HP
\fB\-g\fR, \fB\-\-permute\-axes\fR doPermute
.IP
Permute (or swap) the axes of the individual slice images.
.HP
\fB\-h\fR
.IP
Print the help menu (short version).
.HP
\fB\-\-help\fR
.IP
Print the help menu.
<VALUES>: 1