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mia-3dgetslice(1) | General Commands Manual | mia-3dgetslice(1) |
NAME¶
('mia\-3dgetslice',) - Extract slices from a 3D image.SYNOPSIS¶
mia-3dgetslice -i <in-file> -o <out-file> [options]DESCRIPTION¶
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.OPTIONS¶
- -i --in-file=(input, required); io
- input image(s) to be filtered For supported file types see PLUGINS:3dimage/io
- -o --out-file=(output, required); io
- output image(s). If number != 1 than this is used as a base name and should be given without extension since this will be based on the '--type' option. If number=1 then this exact file name will be used. For supported file types see PLUGINS:2dimage/io
- -t --type=png
- output file type for number != 1
Supported values are:( bmp, datapool, dicom, exr,
jpg, png, raw, tif, vista, )
- -s --start=0
- start slice number
- -n --number=1
- number of slices (all=0)
- --ndigits=4
- minimum number of digits of the file name numbers (if n != 1)
- -d --dir=xy
- slice direction (xy=axial, xz=coronal, yz=saggital)
xz ‐ get xz (coronal) slice
yz ‐ get yz (saggital) slice
xy ‐ 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 ‐ Low level messages
trace ‐ Function call trace
fail ‐ Report test failures
warning ‐ Warnings
error ‐ Report errors
debug ‐ Debug output
message ‐ Normal messages
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: 2dimage/io¶
- bmp
- BMP 2D-image input/output support. The plug-in supports reading and writing of binary images and 8-bit gray scale images. read-only support is provided for 4-bit gray scale images. The color table is ignored and the pixel values are taken as literal gray scale values.
('Recognized file extensions: ', '.BMP, .bmp')
Supported element types:
binary data, unsigned 8 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
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¶
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
AUTHOR(s)¶
Gert WollnyCOPYRIGHT¶
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'.v2.4.6 | USER COMMANDS |