mia-3dgetslice (1)

mia-3dgetslice -i <in-file> -o <out-file> [options]

mia-3dgetslice This program is used to extract 2D slices from a 3D data set and store them in separate files. Output files will be numbered according to their slice index.

-i --in-file=(input,required)

input image(s) to be filtered For supported file types see PLUGINS:3dimage/io

-o --out-file=(output,required)

output image(s) base name, give without extension since this will be based on the '--type' option For supported file types see PLUGINS:2dimage/io

-t --type=png

output file type

-s --start=0

start slice number

-n --number=0

number of slices (all=0)

--ndigits=4

minimum number of digits of the file name numbers

-d --dir=xy

slice direction (xy=axial, xz=coronal, yz=saggital)

xz \(hy get xz (coronal) slice

yz \(hy get yz (saggital) slice

xy \(hy get xy (axial) slice

Help & Info

-V --verbose=warning

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

info \(hy Low level messages

trace \(hy Function call trace

fail \(hy Report test failures

warning \(hy Warnings

error \(hy Report errors

debug \(hy Debug output

message \(hy Normal messages

fatal \(hy 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).

bmp

BMP 2D-image input/output support

Recognized file extensions: .BMP, .bmp

Supported element types:

binary data, unsigned 8 bit, unsigned 16 bit

datapool

Virtual IO to and from the internal data pool

Recognized file extensions: .@

dicom

2D image io for DICOM

Recognized file extensions: .DCM, .dcm

Supported element types:

signed 16 bit, unsigned 16 bit

exr

a 2dimage io plugin for OpenEXR images

Recognized file extensions: .EXR, .exr

Supported element types:

unsigned 32 bit, floating point 32 bit

jpg

a 2dimage io plugin for jpeg gray scale images

Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg

Supported element types:

unsigned 8 bit

png

a 2dimage io plugin for png images

Recognized file extensions: .PNG, .png

Supported element types:

binary data, unsigned 8 bit, unsigned 16 bit

raw

RAW 2D-image output support

Recognized file extensions: .RAW, .raw

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

tif

TIFF 2D-image input/output support

Recognized file extensions: .TIF, .TIFF, .tif, .tiff

Supported element types:

binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

vista

a 2dimage io plugin for vista images

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

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, 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

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, 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:

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

Store 5 coronal slices starting at slice 120 coronalXXXX.png from image.v. mia-3dgetslice -i image.v -o coronal -t png -n 5 -s 120

Gert Wollny

This software is Copyright (c) 1999\(hy2013 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'.