brede_vol - Overview of volume functions
Functions:
brede_vol_abs - Absolute values of voxels
brede_vol_add - Add two volumes
brede_vol_and - Binary AND of volumes
brede_vol_assign2label - Convert assignent volumes to labeled
brede_vol_binarize - Binarize volume (one or zero)
brede_vol_center - Center of volume
brede_vol_density2prob - Convert densities to probabilities
brede_vol_flood - Binary flooding operation
brede_vol_gencoord - Generate volume coordinates
brede_vol_mask - Find a mask from a series of volumes
brede_vol_mat2vol - Convert matrix to 'vol' structure
brede_vol_negate - Negate voxel values
brede_vol_not - Binary inversion of voxel values
brede_vol_or - Binary OR on volumes
brede_vol_origin - Report the origin
brede_vol_plot_cumdist - Plot cummulative distribution
brede_vol_plot_hist - Plot histogram of voxel values
brede_vol_product - Multiplication of volumes
brede_vol_range - Range of volume in x, y and z
brede_vol_regident - Region identification
brede_vol_register - Image registration
brede_vol_resample - Spatial resampling
brede_vol_scale - Scale voxel-value in volume
brede_vol_smooth - Spatial smoothing
brede_vol_subtract - Subtract one vol from another
brede_vol_threshold - Thresholding based on voxel values
brede_vol_twosample - Two-sample test between to sets
brede_vol_vol2exp - Convert 'vol' to 'exp' structure
brede_vol_vol2loc - Find locations in a volume
brede_vol_vol2mat - Convert 'vol' to 'mat' structure
brede_vol_vol2sur - Convert 'vol' to 'sur' structure
brede_vol_vol2vol - Clean a 'vol' structure
brede_vol_vol2vrml - Make VRML model of volume
brede_vol_vols2html - Convert volumes to HTML
brede_vol_xform - Transform volume to an other space
brede_read_analyze - Set 'vol' structure from Analyze file
brede_read_xml2vol - Read XML with volume
brede_ta2_vol - Plot slices from a volume in 2D
brede_ta3_volslice - Plot a slice from a volume in 3D
brede_ta3_volsurf - Plot an isosurface of a volume
brede_ui_vol - Graphical user interface for volumes
brede_write_analyze - Write an Analyze file
brede_write_xml2vol - Write volume to XML file
Functions with the brede_vol_ prefix handles the 'vol'
structure which contains a volume in stereotactic space along
with description of it.
The volume should be oriented so the lower, left and back
corner voxel is the first element in the array.
The volume is stored in the 3-dimensional array in the
V.volume field. V.x, V.y and V.z should each be set with a
vector to the center of each plane.
The 'vol' structure
V.type = 'vol' Fixed field
V.Bib 'Bib' structure if the volume is
associated with bibliographic information
V.description Textural description of the volume
V.filename Filename if the volume is associated
with a file.
V.origin Origin in voxel index
V.volume The volume as a 3D matrix (array)
V.voxelSize Voxel size in meter
V.x Coordinates where x-planes appear
V.y Coordinates where y-planes appear
V.z Coordinates where z-planes appear
Example:
% Read cerebellum mask
f = fullfile(fileparts(which('brede')), 'xml', 'cerebellum1.xml');
Vcerebellum = brede_read_xml2vol(f);
% Invert cerebellum mask
Vnotcerebellum = brede_vol_not(Vcerebellum);
% Read brain mask
f = fullfile(fileparts(which('brede')), 'xml', 'brainmask1.xml');
Vbrainmask = brede_read_xml2vol(f);
% Subtract the cerebellum mask from the brain mask
Vbrain_without_cerebellum = brede_vol_and(Vbrainmask, Vnotcerebellum)
% Render the resulting brain mask
brede_ta2_vol(Vbrain_without_cerebellum)
See also BREDE, BREDE_BIB, BREDE_BM, BREDE_EXP, BREDE_LOC,
BREDE_MAT, BREDE_STR, BREDE_VOL_ABS, BREDE_VOL_ADD,
BREDE_VOL_AND, BREDE_VOL_ASSIGN2LABEL,
BREDE_VOL_BINARIZE, BREDE_VOL_CENTER,
BREDE_VOL_DENSITY2PROB, BREDE_VOL_FLOOD,
BREDE_VOL_GENCOORD, BREDE_VOL_MASK, BREDE_VOL_MAT2VOL,
BREDE_VOL_NEGATE, BREDE_VOL_NOT, BREDE_VOL_ORIGIN,
BREDE_VOL_PLOT_CUMDIST, BREDE_VOL_PLOT_HIST,
BREDE_VOL_OR, BREDE_VOL_RANGE, BREDE_VOL_REGIDENT,
BREDE_VOL_REGISTER, BREDE_VOL_RESAMPLE,
BREDE_VOL_SCALE, BREDE_VOL_SUBTRACT,
BREDE_VOL_THRESHOLD, BREDE_VOL_TWOSAMPLE,
BREDE_VOL_VOL2EXP, BREDE_VOL_VOL2LOC,
BREDE_VOL_VOL2MAT, BREDE_VOL_VOL2VOL, BREDE_VOL_XFORM,
BREDE_VOL_VOLS2HTML, BREDE_TA2_VOL,
BREDE_TA3_VOLSURF, BREDE_TA3_VOLSLICE,
BREDE_UI_VOL, BREDE_WRITE_ANALYZE.
$Id: brede_vol.m,v 1.19 2008/06/30 19:47:07 fn Exp $