New subject: Monte Carlo Simulation Precomputed Data

28 Jan 2014

      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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-- 
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Monte Carlo Simulation Precomputed Data