---
name: "mia-3dcrispsegment"
section: "1"
platform: "linux"
package: "mia-tools"
version: "2.4.7-11+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/mia-3dcrispsegment"
---

# mia-3dcrispsegment(1)

Label segmentation according to probabilities.

## NAME

mia-3dcrispsegment - Label segmentation according to probabilities.

## SYNOPSIS

**mia-3dcrispsegment -i \<in-file\> -o \<out-file\> \[options\]**

## DESCRIPTION

**mia-3dcrispsegment** This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the higest probability plus a given offset

## OPTIONS

- \-i --in-file=(required, input); io

  input class file, should contain multiple images with tissue class probabilities\
    For supported file types see PLUGINS:3dimage/io

- \-o --out-file=(required, output); io

  output class label image\
    For supported file types see PLUGINS:3dimage/io

- \-l --label-offset=1

  label offset

### Help & Info

- \-V --verbose=warning

  verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

  *trace* ‐ Function call trace

  *debug* ‐ Debug output

  *info* ‐ Low level messages

  *message* ‐ Normal messages

  *warning* ‐ Warnings

  *fail* ‐ Report test failures

  *error* ‐ Report errors

  *fatal* ‐ Report only fatal errors

- \--copyright

  print copyright information

- \-h --help

  print this help

- \-? --usage

  print a short help

- \--version

  print the version number and exit

### Processing

- \--threads=-1

  Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

## PLUGINS: 3dimage/io

- **analyze**

  Analyze 7.5 image

Recognized file extensions:  .HDR, .hdr

Supported element types:

unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit

- **datapool**

  Virtual IO to and from the internal data pool

Recognized file extensions:  .@

- **dicom**

  Dicom image series as 3D

Recognized file extensions:  .DCM, .dcm

Supported element types:

signed 16 bit, unsigned 16 bit

- **hdf5**

  HDF5 3D image IO

Recognized file extensions:  .H5, .h5

Supported element types:

binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit

- **inria**

  INRIA image

Recognized file extensions:  .INR, .inr

Supported element types:

signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

- **mhd**

  MetaIO 3D image IO using the VTK implementation (experimental).

Recognized file extensions:  .MHA, .MHD, .mha, .mhd

Supported element types:

signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

- **nifti**

  NIFTI-1 3D image IO. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package.

Recognized file extensions:  .NII, .nii

Supported element types:

signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit

- **vff**

  VFF Sun raster format

Recognized file extensions:  .VFF, .vff

Supported element types:

unsigned 8 bit, signed 16 bit

- **vista**

  Vista 3D

Recognized file extensions:  .-, .V, .VISTA, .v, .vista

Supported element types:

binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

- **vti**

  3D image VTK-XML in- and output (experimental).

Recognized file extensions:  .VTI, .vti

Supported element types:

signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

- **vtk**

  3D VTK image legacy in- and output (experimental).

Recognized file extensions:  .VTK, .VTKIMAGE, .vtk, .vtkimage

Supported element types:

signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit

## EXAMPLE

Set the labels based on the input class probability file cls.v adding the offset 2 to each label and save the result to labeled.v.

mia-3dcrispsegment -i cls.v -o labeled.v -l 2

## AUTHOR(s)

Gert Wollny

## COPYRIGHT

This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain. It comes  with  ABSOLUTELY  NO WARRANTY  and  you  may redistribute it under the terms of the GNU  GENERAL PUBLIC LICENSE Version 3 (or later). For more  information run the program with the option '--copyright'.