MINCMORPH(1)

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