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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 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> > 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> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the > person to > whom it is > addressed. If you believe this e-mail was sent to you in > error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: 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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
