NAME
mincmorph - MNI medical image format tools
SYNOPSIS
mincmorph [options] <in.mnc> <out.mnc>
DESCRIPTION
Command-specific options: General options:
- -verbose:
-
be verbose
- -clobber:
-
clobber existing files
Outfile Options
- -filetype:
-
Use data type of the input file.
- -byte:
-
Write out byte data.
- -short:
-
Write out short integer data. (Default)
- -int:
-
Write out long integer data.
- -float:
-
Write out single-precision data.
- -double:
-
Write out double-precision data.
- -signed:
-
Write signed integer data.
- -unsigned:
-
Write unsigned integer data.
Kernel Options
- -2D04:
-
Use a 2D 4-connectivity kernel.
- -2D08:
-
Use a 2D 8-connectivity kernel.
- -3D06:
-
Use a 3D 6-connectivity kernel. (default)
- -3D26:
-
Use a 3D 26-connectivity kernel.
- -kernel:
-
<kernel.kern> read in a custom kernel file
Morphology Options
- -floor:
-
lowwer value for binarising or clamping
-
Default value: -1.79769e+308
- -ceil:
-
upper value for binarising or clamping (incl)
-
Default value: 1.79769e+308
- -range:
-
range for binarising or clamping (incl)
-
Default value: -1.79769e+308 1.79769e+308
- -foreground:
-
foreground value
-
Default value: 1
- -background:
-
background value
-
Default value: 0
Single morphological operations:
- -binarise:
-
binarise volume using the input range
- -clamp:
-
clamp volume using the input range
- -pad:
-
pad volume with respect to the current kernel (-background to specify value)
- -erosion:
-
do a single erosion
- -dilation:
-
do a single dilation
- -median_dilation:
-
do a single median dilation (note: this is not a median filter!)
- -open:
-
open: dilation(erosion(X))
- -close:
-
close: erosion(dilation(X))
- -lowpass:
-
lowpass filter: close(open(X))
- -highpass:
-
highpass filter: X - lowpass(X)
- -convolve:
-
convolve file with kernel
- -distance:
-
distance transform
- -group:
-
label groups in ascending order
Successive morphological operations:
- -successive:
-
Successive operations (Maximum: 100)
-
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"
Generic options for all commands:
- -help:
-
Print summary of command-line options and abort
- -version:
-
Print version number of program and exit
-
mincmorph -help