mia-3dimagestats(1)

Usage

mia-3dimagestats -i <in-file> [options]

Overview

mia-3dimagestats This program is used to evaluate certain image statistics and print them out on the console.

Options

-i --in-file=(required, input); io: input image(s) to be filtered
For supported file types see PLUGINS:3dimage/io

-t --thresh=10: intensity thresh to ignore

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

Examples

Evaluate the statistics of image input.v and ignore all voxels with an intensity below 5.

mia-3dimagestats -i input.v -t 5

AUTHOR(s)

Gert Wollny

History

Debian 12 (Bookworm) to Debian 11 (Bullseye): the text shown here
Debian 10 (Buster)
Debian 9 (Stretch)
Debian 8 (Jessie)