MINCMORPH

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