SliceOverlayHelp32013-03-07 21:22:55localhostconverted to 1.6 markup22006-08-24 10:57:53devel03.mrc-cbu.cam.ac.uk12006-08-24 10:57:29devel03.mrc-cbu.cam.ac.ukHelp for slice_overlay scriptThis 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.
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'
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