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 <sim...@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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