= Help for slice_overlay script = This is just the help documentation from the `slice_overlay` routine, described in the DisplaySlices page. The same help results from typing `help slice_overlay` at the matlab prompt. {{{ Function to display + manage slice display Slice display works on a global structure SO with fields - img - array of images to display - img structs contain fields type - one of {'truecolour' 'split', 'contour'}; truecolour - displays transparent (see prop) image overlaid with any previous split - in defined area, replaces image present (SPM type activation display) contour - contour map of image overlaid. See help for contours function in matlab vol - vol struct info (see spm_vol) can also be vol containing image as 3d matrix set with slice_overlay('AddBlobs'...) call cmap - colormap for this image nancol - color for NaN. If scalar, this is an index into the image cmap. If 1x3 vector, it's a colour prop - proportion of intensity for this cmap/img func - function to apply to image before scaling to cmap (and therefore before min/max thresholding. E.g. a func of 'i1(i1==0)=NaN' would convert zeros to NaNs range - 2x1 vector of values for image to distribute colormap across the first row of the colormap applies to the first value in 'range', and the last value to the second value in 'range' outofrange - behavior for image values to the left and right of image limits in 'range'. Left means colormap values < 1, i.e for image values < range(1), if (range(1) range(1) where (range(1)>range(2)). If missing, display min (for Left) and max (for Right) value from colormap. Otherwise should be a 2 element cell array, where the first element is the colour value for image values left of 'range', and the second is for image values right of 'range'. Scalar values for colour index the colormap, 3x1 vectors are colour values. An empty array attracts default settings appropriate to the mode - i.e. transparent colour (where SO.type is truecolour), or split colour. Empty cells default to 0. 0 specifies that voxels with this colour do not influence the image (split = background, true = black) hold - resampling order for image (see spm_sample_vol) - default 1 background - value when resampling outside image - default NaN linespec - string, applies only to contour map, e.g. 'w-' for white continuous lines contours - vector, applies to contour map only, defines values in image for which to show contours (see help contours) linewidth - scalar, width in points of contour lines - transform - either - 4x4 transformation to apply to image slice position, relative to mm given by slicedef, before display or - text string, one of axial, coronal, sagittal These orientations assume the image is currently (after its mat file has been applied) axially oriented - slicedef - 2x3 array specifying dimensions for slice images in mm where rows are x,and y of slice image, and cols are neg max dim, slice separation and pos max dim - slices - vector of slice positions in mm in z (of transformed image) - figure - figure handle for slice display figure - refreshf - flag - if set or empty, refresh axis info for figure else assume this is OK - clf - flag, non zero -> clear figure before display. Redundant if refreshf == 0 - area struct with fields position - bottom left, x size y size 1x4 vector of area in which to display slices units - one of inches,centimeters,normalized,points,{pixels} halign - one of left,{center},right valign - one of top,{middle},bottom - xslices - no of slices to display across figure (defaults to an optimum) - cbar - if empty, missing, no colourbar. If an array of integers, then indexes img array, and makes colourbar for each cmap for that img. Cbars specified in order of appearance L->R - labels - struct can be absent (-> default numerical labels) empty (SO.labels = []) (no labels) or contain fields colour - colour for label text size - font size in units normalized to slice axes format - if = cell array of strings = labels for each slice in Z. If is string, specifies sprintf format string for labelling in distance of the origin (Xmm=0, Ymm=0) of each slice from plane containing the AC, in mm, in the space of the transformed image - callback - callback string for button down on image panels. E.g. setting SO.callback to 'slice_overlay(''getpos'')' prints to the matlab window the equivalent position in mm of the position of a mouse click on one of the image slices - printstr - string for printing slice overlay figure window, e.g. 'print -dpsc -painters -noui' (the default) - printfile - name of file to print output to; default 'slices.ps' FORMAT slice_overlay Checks, fills SO struct (slice_overlay('checkso')), and displays slice overlay (slice_overlay('display')) FORMAT slice_overlay('checkso') Checks SO structure and sets defaults FORMAT [cmap warnstr] = slice_overlay('getcmap',cmapname) Gets colormap named in cmapname string FORMAT [mx mn] = slice_overlay('volmaxmin', vol) Returns maximum and minimum finite values from vol struct 'vol' FORMAT slice_overlay('addspm',SPM,VOL,dispf) Adds SPM blobs as new img to SO struct, split effect, 'hot' colormap, Structures SPM and VOL are generated by calls to SPM results if not passed, they are fetched from the workspace If dispf is not passed, or nonzero, displays resulting SO figure also FORMAT slice_overlay('addblobs', imgno, XYZ, vals, mat) adds SPM blobs to img no 'imgno', as specified in XYZ - 3xN voxel coordinates of N blob values vals - N blob intensity values mat - 4x4 matrix specifying voxels -> mm FORMAT vol = slice_overlay('blobs2vol', XYZ, vals, mat) returns (pseudo) vol struct for 3d blob volume specified in matrices as above FORMAT slice_overlay('addmatrix', imgno, mat3d, mat) adds 3d matrix image vol to img imgno. Optionally mat - 4x4 matrix specifying voxels -> mm FORMAT vol = slice_overlay('matrix2vol', mat3d, mat) returns (pseudo) vol struct for 3d matrix input matrices as above FORMAT mmpos = slice_overlay('getpos') returns equivalent position in mm of last click on current axes (gca) if the axes contain an image slice (empty otherwise) FORMAT vals = slice_overlay('pointvals', XYZmm, holdlist) returns IxN matrix with values of each image 1..I, at each point 1..N specified in 3xN mm coordinate matrix XYZmm If specified, 'holdlist' contains I values giving hold values for resampling for each image (see spm_sample_vol) FORMAT slice_overlay('display') Displays slice overlay from SO struct FORMAT slice_overlay('print', filename, printstr) Prints slice overlay figure, usually to file. If filename is not passed/empty gets filename from SO.printfile. If printstr is not passed/empty gets printstr from SO.printstr V 0.9 8/9/00 Added contour maps (many thanks to Petr Janata for this idea), expanded colormap reader This program is copyright, or rather copyleft, under the terms of the GNU public licence; see licence.man or http://www.gnu.org/copyleft Still beta - take care. Please report problems to Matthew Brett matthew@mrc-cbu.cam.ac.uk }}} MatthewBrett