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