.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
.TH MINCMORPH "1" "July 2020" "mincmorph 2.3.00" "User Commands"
.SH NAME
mincmorph \- MNI medical image format tools
.SH SYNOPSIS
.B mincmorph
[\fI\,options\/\fR] \fI\,<in.mnc> <out.mnc>\/\fR
.SH DESCRIPTION
Command\-specific options:
General options:
.TP
\fB\-verbose\fR:
be verbose
.TP
\fB\-clobber\fR:
clobber existing files
.PP
Outfile Options
.TP
\fB\-filetype\fR:
Use data type of the input file.
.TP
\fB\-byte\fR:
Write out byte data.
.TP
\fB\-short\fR:
Write out short integer data. (Default)
.TP
\fB\-int\fR:
Write out long integer data.
.TP
\fB\-float\fR:
Write out single\-precision data.
.TP
\fB\-double\fR:
Write out double\-precision data.
.TP
\fB\-signed\fR:
Write signed integer data.
.TP
\fB\-unsigned\fR:
Write unsigned integer data.
.PP
Kernel Options
.TP
\fB\-2D04\fR:
Use a 2D 4\-connectivity kernel.
.TP
\fB\-2D08\fR:
Use a 2D 8\-connectivity kernel.
.TP
\fB\-3D06\fR:
Use a 3D 6\-connectivity kernel. (default)
.TP
\fB\-3D26\fR:
Use a 3D 26\-connectivity kernel.
.TP
\fB\-kernel\fR:
<kernel.kern> read in a custom kernel file
.PP
Morphology Options
.TP
\fB\-floor\fR:
lowwer value for binarising or clamping
.IP
Default value: \fB\-1\fR.79769e+308
.TP
\fB\-ceil\fR:
upper value for binarising or clamping (incl)
.IP
Default value: 1.79769e+308
.TP
\fB\-range\fR:
range for binarising or clamping (incl)
.IP
Default value: \fB\-1\fR.79769e+308 1.79769e+308
.TP
\fB\-foreground\fR:
foreground value
.IP
Default value: 1
.TP
\fB\-background\fR:
background value
.IP
Default value: 0
.SS "Single morphological operations:"
.TP
\fB\-binarise\fR:
binarise volume using the input range
.TP
\fB\-clamp\fR:
clamp volume using the input range
.TP
\fB\-pad\fR:
pad volume with respect to the current kernel (\fB\-background\fR to specify value)
.TP
\fB\-erosion\fR:
do a single erosion
.TP
\fB\-dilation\fR:
do a single dilation
.TP
\fB\-median_dilation\fR:
do a single median dilation (note: this is not a median filter!)
.TP
\fB\-open\fR:
open:            dilation(erosion(X))
.TP
\fB\-close\fR:
close:           erosion(dilation(X))
.TP
\fB\-lowpass\fR:
lowpass filter:  close(open(X))
.TP
\fB\-highpass\fR:
highpass filter: X \- lowpass(X)
.TP
\fB\-convolve\fR:
convolve file with kernel
.TP
\fB\-distance\fR:
distance transform
.TP
\fB\-group\fR:
label groups in ascending order
.SS "Successive morphological operations:"
.TP
\fB\-successive\fR:
Successive operations (Maximum: 100)
.IP
B[floor:ceil:fg:bg] \- binarise in the range, using foreground and background
K[floor:ceil:bg] \- clamp between the specified range. Set other voxels to 'bg' (default: 0)
P[bg] \- pad volume with respect to the current kernel using 'bg' (default: 0)
E \- erosion
D \- dilation
M \- median dilation
O \- open
C \- close
L \- lowpass filter
H \- highpass filter
X \- convolve
F \- distance transform (binary input only \- not checked)
G \- Label the groups in the volume in ascending order
R[TYPE|file.kern] \- (2D04|2D08|3D06|3D26) or read in a kernel file
W[file.mnc] \- write out current results
I[cmp.mnc] \- local xcorr between current file and cmp.mnc
Default:  "B"
.SS "Generic options for all commands:"
.TP
\fB\-help\fR:
Print summary of command\-line options and abort
.TP
\fB\-version\fR:
Print version number of program and exit
.IP
mincmorph \fB\-help\fR