Hi Simon
I just took a look at the code and I believe that we make it 0 median (not mean) and unit standard deviation. The curvatures can get quite large in regions where the vertex spacing is small and the median is robust to this.
cheers Bruce
On Sat, 24 Oct 2015, Simon Vandekar wrote:
Hi Bruce,
I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere.
Thanks again, Simon
H I Simon Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it Bruce
On Oct 22, 2015, at 3:23 PM, Simon Vandekar simonv@mail.med.upenn.edu wrote:
Hi Bruce,
I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)?
sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc'))
mean(sulc$sulc)
[1] -1.236923e-08
var(sulc$sulc)
[1] 0.3276958
quantile(sulc$sulc)
0% 25% 50% 75% 100%-1.72503 -0.42128 -0.03963 0.40072 1.80980
Thanks again, Simon
Hi Simon
they are originally mm, but I believe we z-score normalize them so that the sulc file is 0 mean and unit variance.
cheers Bruce On Wed, 21 Oct 2015, Simon Vandekar wrote:
Dear Freesurfer experts,
I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. Are the units for sulcal depth in mm or are they in arbitrary units?
Thanks in advance, Simon
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