mincmorph1
Mni medical image format tools
Usage
mincmorph [options]
<in.mnc>
<out.mnc>
Overview
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 (
-backgroundto 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