subdivide-brain-image

Synopsis

subdivide-brain-image [<input>] <output> [options]
subdivide-brain-image [options]

Description

This program reads a structural brain segmentation and derives from it a segmentation of the brain volume into the following output labels. This output segmentation can then be used to reconstruct topologically correct (i.e., closed genus-0) surfaces of the cGM/WM interface for the left and right hemisphere, where subcortical and deep brain structures are enclosed by these so-called white surfaces. Additionally, the brainstem+cerebellum segment can be respresented by another closed surface mesh. The union of these reconstructured surfaces encloses the entire brain volume, yet excluding cortical grey matter. By deforming the joint brain surface towards the cGM/CSF interface, the pial surface which encloses the entire brain volume including subcortical structures can be obtained. The right/left hemisphere assignment of cortical grey matter follows from the point correspondences between white and pial surfaces, respectively, the RH/LH label may be assigned to white surface mesh nodes upon merging the right/left white surface meshes. See merge-surfaces -source-array option.

Output labels: - 0: Background - 1: Cortical grey matter - 2: Cerebral white matter and deep brain structures of right hemisphere - 3: Cerebral white matter and deep brain structures of left hemisphere - 4: Brainstem, including cerebellum when subdivide-brain-image -brainstem-and-cerebellum is on - 5: Cerebellum, when subdivide-brain-image -brainstem-and-cerebellum is off

Arguments

input

Input label image. See -input-labels.

output

Output label image. See -output-labels.

Command options

-input-labels, -input <file>

Input segmentation label image, use either this option or <input> argument. For each of the following options which take a <labels> argument, the respective segmentation mask is derived from this input label image by merging the specified segments of this brain segmentation. Multiple integer labels can be specified as the <labels> argument, each separated by at least one space character. A range of labels can be specified as <first>..<last>. When the <labels> argument is a single argument that is neither an integer nor a label range, the argument is expected to be the name of a binary mask image file. This option is required when any of the other options has one or more <labels> arguments. It is ignored otherwise. (default: none)

-output-labels, -output <file>

Output label image, use either this option or <output> argument.

-hemispheres <file>

Hemispheres mask (0: outside, 1: right, 2: left) from which cutting plane is computed. (default: none)

-right-hemisphere, -rh <file>|<labels>

Mask or labels of structures of right hemisphere used to compute cutting plane. This option is required when no -hemispheres mask is given.

-left-hemisphere, -lh <file>|<labels>

Mask or labels of structures of left hemisphere used to compute cutting plane. This option is required when no -hemispheres mask is given.

-subcortical, -sb <file>|<labels>

Subcortical / deep brain structures segmentation mask or labels. When specified, these structures are cut into RH and LH. (default: none)

-white-matter, -wm <file>|<labels>

White matter segmentation mask or labels. (default: none)

-grey-matter, -gm <file>|<labels>

Grey matter segmentation mask or labels. (default: none)

-brainstem, -bs <file>|<labels>

Brainstem segmentation mask or labels. (default: none)

-cerebellum, -cb <file>|<labels>

Cerebellum segmentation mask or labels. (default: none)

-closing, -closing-iterations <n>

No. of iterations used to close holes between right/left subcortical, brainstem, and cerebellum segmentations. (default: 0)

-subcortical-closing <n>

No. of iterations used to close holes between right/left subcortical segmentation. (default: 0)

-brainstem-closing <n>

No. of iterations used to close holes in brainstem segmentation. (default: 0)

-cerebellum-closing <n>

No. of iterations used to close holes in cerebellum segmentation. (default: 0)

-brainstem-and-cerebellum, -cerebellum-and-brainstem, -bscb, -cbbs [on|off]

Whether to merge brainstem and cerebellum. (default: off)

Standard options

-v, -verbose [n]

Increase/Set verbosity of output messages. (default: 0)

-debug [level]

Increase/Set debug level for output of intermediate results. (default: 0)

-version [major.minor]

Print version and exit or set version to emulate.

-revision

Print revision (or version) number only and exit.

-h, -help

Print help and exit.