On Tue, Jan 28, 2014 at 12:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Natasha, please remember to post to the list! When you say a different set of blobs, do you mean that none of the original blobs are there? Or do some of the blobs just disappear? Note that the threshold you use in the simulation is not related to the "Threshold Min". In this case, the Threshold Min is the corrected threshold (clusterwise). The threshold used in the simulation is the "cluster forming threshold"

doug

On 01/28/2014 02:51 PM, Natasha Haris wrote:

Thank you! Additionally, after running the clusterwise Monte carlo simulation with p<0.01 I get a blob. After placing this value in the threshold min box I get a different set of blobs on my image. Why is this?

Natasha

On Tue, Jan 28, 2014 at 11:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Yes, when looking at the corrected images, the Threshold Min
because the clusterwise threshold. So if you want to see only
clusters that have a clusterwise p<.05, set that threshold to 1.3

doug

On 01/28/2014 02:24 PM, Natasha Haris wrote:

The clusterwise simulation runs with a p<0.05 threshold value
and a blob appears. However, am I supposed to enter this
threshold value corresponding to p<0.05 (namely 1.3) into the
box labeled threshold min= ?

On Mon, Jan 27, 2014 at 8:43 AM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

On 01/24/2014 11:54 AM, Natasha Haris wrote:
> Dear Freesurfers,
>
> I am slightly confused about the monte carlo simulation.
>
> First off, I only find a blob when I run the p<0.05
threshold
level and don't see anything else when I run simulations
with p
less than that. What does this mean?
Which threshold level? clusterforming/voxelwise or
clusterwise? If
clusterwise, then it just means that you have a cluster
whose p
value is
just under .05 so you lose it by going to a more stringent
threshold.
>
> Additionally, when I click on any question of interest after
running this p<0.05 simulation (for ex. "Does the average
thickness, accounting for Group, differ between male and
female?"
I get the same blobs that I found before I ran this
precomputed
simulation. Is the simulation not running correctly? Am I
supposed
to enter this threshold value (1.3) into the area marked
Threshold
min= and max=5.
Are you sure it is exactly the same? Look to see if there
are some
very
small blobs that disappear. Otherwise, it may be that the
blobs
you have
are all significant.
>
> Thank you for your help!
> Natasha
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