project-onto-surface

Synopsis

project-onto-surface <input> <output> -image <file> [options]
project-onto-surface <input> <output> -labels <file> [options]
project-onto-surface <input> <output> -constant <value>... [options]
project-onto-surface <input> <output> -surface <file> [-scalars <scalars> [<scalars_new_name>] ]
project-onto-surface <input> <output> -boundary [-nolabel-points] [-nolabel-cells] [-name <scalars>]

Description

Assign scalars or labels to either the vertices or the cells of a surface mesh. When the input is a real-valued image, the values are linearly interpolated. When the input is a segmentation image, the value assigned to a vertex/cell is the label of the nearest voxel in the given segmentation image. For the projection of cortical labels onto the WM/GM or GM/CSF boundary, use project-onto-surface -white or project-onto-surface -pial.

Arguments

input

Input surface mesh.

output

Output surface mesh.

Command options

-white

Input surface is cortical WM/GM boundary. (default: off)

-pial

Input surface is cortical GM/CSF boundary. (default: off)

-image <file>

Input real-valued scalar/vector image.

-labels <file>

Input segmentation image with positive integer labels.

-surface <file>

Input surface from which to project scalars.

-constant <value>...

Assign tuple of constant values to all points/cells.

-name <name>

Name of output scalar array. (default: Scalars or Labels)

-type char|uchar|short|ushort|int|uint|float|double

Type of output scalar array. (default: float)

-celldata, -nocelldata

Assign values to cells of input surface. (default: off)

-pointdata, -nopointdata

Assign values to points of input surface. (default: on)

-fill, -nofill

Fill holes/small patches in projected surface parcellation. (default: on)

-max-hole-size <n>

Only fill in holes with less than or exactly n points/cells. When non-positive, the largest -n holes are kept. A zero value is equivalent to -1, i.e., only the largest hole is kept. (default: max value)

-smooth <n>

Number of iterations to smooth. (default: 0)

-min-size <n>

Surface patches with less than n points/cells are removed. When -fill is given, the resulting holes are filled in using the non-zero labels of surrounding patches. Otherwise, the removed patches remain unlabeled (i.e., label value zero). (default: 0)

-min-ratio <ratio>

Keep only components that are larger than ratio times the size of the largest connected component per label, with 0 < ratio <= 1. When -fill is given, the resulting holes are filled in using the non-zero labels of surrounding patches. Otherwise, the removed patches remain unlabeled (i.e., label value zero). (default: 0)

-scalars <input_name> [<output_name>]

Scalars to be projected from the input surface (can be defined multiple times). <name2> can be specified to set the name of the output scalar array.

-boundary

Output boundary lines between surface parcels. (default: off) When no -image or -labels input file is specified, the boundaries of the input parcellation given by the labels array with the specified -name are extracted.

-dilation-radius <float>

Maximum distance of voxel from input label image boundary to be assigned this label during dilation before projecting these labels onto the surface. (default: inf)

-write-dilated-labels <file>

Write image of dilated labels.

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.