Hi Emma,
I might not be the only one who is unsure what you mean by a vertex-wise
cortical surface area measure. Do you mean something like what is illustrated
in figures 2 and 3 here:
http://www.pnas.org/content/107/29/13135.figures-only
… which is similar, but not identical to the local gyr
Hi Alan & Knut,
Isn't GI a function of surface area, i.e. GI = SurfaceAreaPial/SurfaceAreaHull,
e.g.:
http://www.frontiersin.org/files/Articles/668/fninf-03-025/image_m/fninf-03-025-g003.jpg
The hull area (denominator) normalizes for scale, so I would not expect the GI
and surface area to be i
Correction: FI = Sum-over-vertices[ |kmax|(|kmax|-|kmin|)]/SurfaceArea
On Sep 28, 2011, at 1:38 PM, Donna Dierker wrote:
> My understanding is that GI is also a global summary stat across the whole
> hem, while lGI is *local* GI (vertex-wise). It measures how folded the
> cortex i
My understanding is that GI is also a global summary stat across the whole hem,
while lGI is *local* GI (vertex-wise). It measures how folded the cortex is at
that vertex. GI and lGI are based on area, while the folding index is based on
curvature. Truly different measures.
Gyrification Inde
Think in 2D about averaging two sine waves that are shifted 90 degrees
from one another.
The length of of the resulting line will be far less than that of either
curve.
On 05/11/2011 11:20 PM, Michael Waskom wrote:
> Hi Bruce,
>
> I've seen this brought up on the list a few times, and, I have t
I'm not, either, but I think some good brains are working on it (not mine).
Jason Hill and Andy Knutsen developed a semi-automated method:
http://brainvis.wustl.edu/LIGASE/
On 03/31/2011 07:53 AM, Lilla Zollei wrote:
> Hi Adam,
>
> No, Freesurfer is not able to extract the neonatal cortical ribb
This is not my understanding. It is completely dependent on the
threshold used, which can be arbitrary. See Supplemental figure 7, page
16 of this document:
http://www.jneurosci.org/cgi/data/30/6/2268/DC1/1
This was the motivation for Smith & Nichols' TFCE:
http://www.ncbi.nlm.nih.gov/pubmed/1
Derin,
You might try importing the surfaces into Caret for this. It seems like
there are two needs:
* flat cartesian grid (Menu bar: Layers: Borders: Create Cartesian Flat
Analysis Grid Borders (see attached capture)
* 3-D scale markers (Toolbar: D/C: Surface Miscellaneous: Surface
Cartesian
Matt,
I think we just do things differently. We adopted Ziad Saad's concept
of a standard mesh. (Before Ziad conceived it, we didn't do this,
either.) But not everyone does this. My mental model of how others do
things is poor. I recall using mrisp_paint to get some scalars on our
PALS su
FDR is NOT more conservative than cluster-based methods, in general. The
smoother the data, the more conservative FDR is.
In my experience with surface-based data, FDR has been less sensitive
than cluster-based methods -- perhaps because my data was very smooth.
> Stefan Brauns wrote:
>
>> W
e reason to believe otherwise?
>
> thanks
>
> doug
>
> Donna Dierker wrote:
>> Mike Harms tried to explain that to me, but I was missing how the
>> resampling affected the i term. Thanks, Tom, for spelling it out for
>> me. ;-)
>>
>> Fortunately, John
>> to get past i=1). Meaning that as N grows, the min p-value must also
>> shrink to get past i=1. Any way to get around this?
>>
>> thanks
>>
>> doug
>>
>>
>>
>>
>> -- Forwarded message --
>> Date: Fri, 16
ot;just to get past i=1" as you put it in your post.
>
> Rather, you pick the largest p-value that satisfies the relationship,
> meaning that lower (more-significant) p-values may not have necessarily
> satisfied p <= i/V*q for their particular position in the sorted list of
> p-va
I never heard anything on my post here, but it might just be high
surface resolution:
http://www.mail-archive.com/neuro-mult-c...@brainvis.wustl.edu/msg00026.html
On 10/16/2009 09:58 AM, Michael Harms wrote:
> Your FDR analysis sounds correct. You probably have a rather small
> number of "margi
Ben might be using Oliver Lyttelton's mean MNI152 surface (i.e., the
average of all 152 subjects' surfaces on the MNI mesh, as registered
using CIVET).
On 09/09/2009 11:31 AM, Bruce Fischl wrote:
> Hi Ben,
>
> I would be pretty surprised if you can get a reasonable surface from the
> MNI152. I
I haven't experienced this with Freesurfer, but I have had this problem
with Caret using Linux workstations with pre-installed NVIDIA drivers
that were apparently not working correctly. Downloading and
re-installing the NVIDIA driver corrected the problem on my Linux box.
On 09/01/2009 01:32 P
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