mia-3dbrainextractT11
Extract the brain from a 3d t1 mri head image.
Usage
mia-3dbrainextractT1 -i
<in-file>
-o
<out-file>
[options]
Overview
mia-3dbrainextractT1 This program is used to extract the brain from T1 MR images. It first runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image. Then various fiters are run to obtain a white matter segmentation as initial mask that is then used to run a region growing to obtain a mask of the whole brain. Finally, this mask is used to extact the brain from the B0 field corrected images.
Options
- -i --in-file=(input, required); io
-
input image(s) to be segmented
For supported file types see PLUGINS:3dimage/io
- -o --out-file=(output, required); io
-
brain mask
For supported file types see PLUGINS:3dimage/io
- -n --no-of-classes=3
-
number of classes
- -w --wm-class=2
-
index of white matter
- -p --wm-prob=0.7
-
white matter class probability for initial mask creation
- -t --grow-threshold=20
-
intensity threshold for region growing
-
--grow-shape=18n -
neighbourhood mask region growing
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
Create a mask from the input image by running a 5-class segmentation over inpt image input.v and use class 4 as white matter class and store the masked image in masked.v and the B0-field corrected image in b0.v
mia-3dbrainextractT1 -i input.v -n 5 -w 4 -o masked.v
AUTHOR(s)
Gert Wollny
History
- Debian 12 (Bookworm): the text shown here
- Debian 11 (Bullseye)
- Debian 10 (Buster)
- Debian 9 (Stretch)
- Debian 8 (Jessie)