mia-raw2volume

NAME

mia-raw2volume - Convert raw data into a 3D image

SYNOPSIS

mia-raw2volume -i <in-file> -o <out-file> -s <size> [options]

DESCRIPTION

mia-raw2volume This program is used to convert raw data into 3D images with apropriate metadata.

OPTIONS

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

input file name

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

output file name
For supported file types see PLUGINS:3dimage/io

-r --repn=ubyte

input pixel type

bit - binary data
sbyte - signed 8 bit
ubyte - unsigned 8 bit
sshort - signed 16 bit
ushort - unsigned 16 bit
sint - signed 32 bit
uint - unsigned 32 bit
slong - signed 64 bit
ulong - unsigned 64 bit
float - floating point 32 bit
double - floating point 64 bit
none - no pixel type defined

-b --big-endian

input data is big endian

-f --scale=[1,1,1]

scale of input voxels <FX,FY,FZ>

-k --skip=0

skip number of bytes from beginning of file

-s --size=(required); 3dbounds

size of input <NX,NY,NZ>

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

pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr

mia-raw2volume -i data.raw -o image.hdr -s "<10,20,30>" -k "<1.2,2.3,3.4>" -r ushort

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’.