mia-raw2volume1
Convert raw data into a 3d image
Usage
mia-raw2volume -i
<in-file>
-o
<out-file>
-s
<size>
[options]
Overview
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
Examples
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
History
- Debian 12 (Bookworm): the text shown here
- Debian 11 (Bullseye)
- Debian 10 (Buster)
- Debian 9 (Stretch)
- Debian 8 (Jessie)