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peakfind

Finds peaks in 3d slices of 4d images. Adapted from peak_4dfp by Avi
Snyder and peak_nii by Tony Wilson.

Copyright (c) 2012 Washington University
Author: Kevin A. Archie <[email protected]>

All Fortran subroutines in the package were written by Avi Snyder.

This package produces two MATLAB functions (as mex files):

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[peaks, roi] = peakfind(image, mmppixr, centerr, orad, mask, ...)

Produces a list of peaks and an ROI mask image.

image : single-precision 3D image data in which peaks will be identified
mmppixr : single-precision 3-vector of voxel dimensions in mm
centerr : single-precision 3-vector atlas space offset of image
orad : radius of peak ROIs, in mm
mask : mask applied before producing ROI

optional arguments can be specified like this:

[p, r] = peakfind(i, m, c, o, mask, 'vtpos', 0.5, 'vtneg', 0.1);

valid optional arguments are:

vtpos : positive threshold peak value (default 0)
vtneg : negative threshold peak value (default 0)
ntop : maximum number of output peaks (default 1000)
minvox : minimum output ROI voxel count (default 1)
dthresh : maximum distance for merging peaks (default 0)
ctpos : peak curvature threshold for positive peaks (default 0)
ctneg : peak curvature threshold for negative peaks (default 0)

return values are:

peaks: array of peak structures; each peak structure contains fields:
  i : floating point index (i,j,k) of peak center (rederived from x)
  x : floating point location (x,y,z) of peak center in atlas space
  v : value at peak center
  del2v : Laplacian at peak center
  weight : number of peaks consolidated into this peak
  voxels : size of this peak's ROI sphere, in voxels

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blurimg = sphereblur(image, mmppixr, radius)

Blurs the provided image by convolving with a spherical kernel of
specified radius.

image : single-precision 3D image to be blurred
mmppixr : single-precision 3-vector of voxel dimensions in mm
radius : sphere radius, in mm