mia-3dcrispsegment1
Label segmentation according to probabilities.
Usage
mia-3dcrispsegment -i
<in-file>
-o
<out-file>
[options]
Overview
mia-3dcrispsegment This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the higest probability plus a given offset
Options
- -i --in-file=(required, input); io
-
input class file, should contain multiple images with tissue class probabilities
For supported file types see PLUGINS:3dimage/io
- -o --out-file=(required, output); io
-
output class label image
For supported file types see PLUGINS:3dimage/io
- -l --label-offset=1
-
label offset
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
Set the labels based on the input class probability file cls.v adding the offset 2 to each label and save the result to labeled.v.
mia-3dcrispsegment -i cls.v -o labeled.v -l 2
AUTHOR(s)
Gert Wollny
History
- Debian 12 (Bookworm): the text shown here
- Debian 11 (Bullseye)
- Debian 10 (Buster)
- Debian 9 (Stretch)
- Debian 8 (Jessie)