28 Jan
2014
28 Jan
'14
3:58 p.m.
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> <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>>>>> 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> <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>>> <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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. 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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/