On Tue, Jan 28, 2014 at 1:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

The cluster-forming threshold is needed to define what the clusters are. Once you have a cluster forming threshold, you get clusters with a certain size. Given the size, the FWHM, the cluster forming threshold, and the search space, a p-value for the cluster is computed.

On 01/28/2014 03:58 PM, harisnatasha@gmail.com wrote:

So sorry for all the beginner questions. One more.

Then what is the point of running the Monte Carlo simulation with a cluster-forming threshold of p<0.01 or any other threshold for that matter if I already know what the clusterwise threshold min should be?

Natasha

On Jan 28, 2014, at 12:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Yes

On 01/28/2014 03:35 PM, Natasha Haris wrote:
So then how does one determine what should go into the Threshold min box? (If it's usually p<0.05 should the clusterwise corrected Threshold min be 1.3?)

Natasha

On Tue, Jan 28, 2014 at 12:30 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

On 01/28/2014 03:26 PM, Natasha Haris wrote:

Oops sorry!

I guess my question then is, after running the monte carlo
simulation with this cluster-forming threshold (p<0.01), is
there a specific corrected (clusterwise) threshold I can/am
supposed to place in the Threshold min box? Or are these two
not related in any way.

They are not related. The clusterwise threshold is what you would
use when you go to convince a reviewer that the effect is
significant. Usually, this is .05.

Natasha

On Tue, Jan 28, 2014 at 12:11 PM, 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:

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>
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<mailto: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
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<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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