---
name: "mincmorph"
section: "1"
platform: "linux"
package: "minc-tools"
version: "2.3.00+dfsg-12"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mincmorph"
---

# mincmorph(1)

MNI medical image format tools

## 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**