Hi Andreas
I just took a look at the code and it seems you are correct! Thanks for
catching this. I'll change the code base now and the fix will be in v6.
Bruce
On Fri, 22 Jan 2016, Andreas
Schuh wrote:
> Hi,
>
> I studied the FreeSurfer code for MRISinflateBrain and came across a
> discrepa
Hi,
I studied the FreeSurfer code for MRISinflateBrain and came across a
discrepancy in how the sulcal depth is computed. This explains why the values
are much smaller than expected.
My question @Bruce is if this is intentional or (as the function names below
indicate) possibly a bug in the ea
Hi Bruce,
The units are not standardized because the standard deviation across the
surface does not equal 1.
>From line 227 in mris_inflate.c it says that the sulc file is demeaned before
>it is written out:
MRISzeroMeanCurvature(mris) ; /* make sulc zero mean */
However I am still uncle
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
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 wrote:
>
> Hi Bruce,
>
> I chose a random subject from the ADNI dataset and computed the mean and
> variance for the left and right hemis
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 som
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,
> Flat
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 unsur
