mia-3dbrainextractT1 {-i io} {-o io} [
options
...]
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.
input image(s) to be segmented. For supported file types see Plugin type: 3dimage/io
brain mask. For supported file types see Plugin type: 3dimage/io
number of classes
index of white matter
white matter class probability for initial mask creation
intensity threshold for region growing
neighbourhood mask region growing
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:
| debug: | Debug output |
| message: | Normal messages |
| info: | Low level messages |
| error: | Report errors |
| fatal: | Report only fatal errors |
| trace: | Function call trace |
| warning: | Warnings |
| fail: | Report test failures |
print copyright information
print this help
print a short help
print the version number and exit
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).
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
Gert Wollny