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brede_vol

PURPOSE ^

brede_vol - Overview of volume functions

SYNOPSIS ^

This is a script file.

DESCRIPTION ^

 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 $

CROSS-REFERENCE INFORMATION ^

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