7.1.44. 3dAnhist

Link to classic view

Usage: 3dAnhist [options] dataset Input dataset is a T1-weighted high-res of the brain (shorts only). Output is a list of peaks in the histogram, to stdout, in the form

( datasetname #peaks peak1 peak2 ... )

In the C-shell, for example, you could do

set anhist = 3dAnhist **-q** -w1 dset+orig

Then the number of peaks found is in the shell variable $anhist[2].

Options:
-q = be quiet (don’t print progress reports)
-h = dump histogram data to Anhist.1D and plot to Anhist.ps
-F = DON’T fit histogram with stupid curves.
-w = apply a Winsorizing filter prior to histogram scan
(or -w7 to Winsorize 7 times, etc.)
-2 = Analyze top 2 peaks only, for overlap etc.
-label xxx = Use ‘xxx’ for a label on the Anhist.ps plot file
instead of the input dataset filename.
-fname fff = Use ‘fff’ for the filename instead of ‘Anhist’.

If the ‘-2’ option is used, AND if 2 peaks are detected, AND if the -h option is also given, then stdout will be of the form

( datasetname 2 peak1 peak2 thresh CER CJV count1 count2 count1/count2)
where 2 = number of peaks
thresh = threshold between peak1 and peak2 for decision-making CER = classification error rate of thresh CJV = coefficient of joint variation count1 = area under fitted PDF for peak1 count2 = area under fitted PDF for peak2 count1/count2 = ratio of the above quantities

NOTA BENE

  • If the input is a T1-weighted MRI dataset (the usual case), then

    peak 1 should be the gray matter (GM) peak and peak 2 the white matter (WM) peak.

  • For the definitions of CER and CJV, see the paper

    Method for Bias Field Correction of Brain T1-Weighted Magnetic Resonance Images Minimizing Segmentation Error JD Gispert, S Reig, J Pascau, JJ Vaquero, P Garcia-Barreno, and M Desco, Human Brain Mapping 22:133-144 (2004).

  • Roughly speaking, CER is the ratio of the overlapping area of the

    2 peak fitted PDFs to the total area of the fitted PDFS. CJV is (sigma_GM+sigma_WM)/(mean_WM-mean_GM), and is a different, ad hoc, measurement of how much the two PDF overlap.

  • The fitted PDFs are NOT Gaussians. They are of the form

    f(x) = b((x-p)/w,a), where p=location of peak, w=width, ‘a’ is a skewness parameter between -1 and 1; the basic distribution is defined by b(x)=(1-x^2)^2*(1+a*x*abs(x)) for -1 < x < 1.

– RWCox - November 2004

++ Compile date = Dec 16 2015

Table Of Contents

This Page