All vertices in the cluster will have this value. It can be found in the "summary" file in each contrast. It is the final clusterwise p-value, ie, the probability of seeing a cluster of the given size by random chance.
doug
On 01/28/2014 05:07 PM, Natasha Haris wrote:
Where does it appear and what does one make of it?
On Tue, Jan 28, 2014 at 1:58 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
QDEC computes it
On 01/28/2014 04:52 PM, Natasha Haris wrote:
And does the monte carlo precomputed simulation data in the
QDEC GUI compute this final p-value? Or do I need to use any
commands namely mri_glmfit?
On Tue, Jan 28, 2014 at 1:38 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:
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
<mailto:harisnatasha@gmail.com>
<mailto:harisnatasha@gmail.com
<mailto: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
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto: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>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto: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 01/28/2014 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>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto: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>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<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
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto: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
>
_______________________________________________
> Freesurfer
mailing list
>
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>>
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve,
Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto: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>>>>
<mailto:greve@nmr.mgh.harvard.edu
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<mailto: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
<mailto:greve@nmr.mgh.harvard.edu>>>>>>
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<tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
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<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>>>>
Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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