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 <gr...@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 <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@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 >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@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 >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto: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>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> >> <mailto: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>> >> <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. 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>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> >> <mailto: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>> >> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 >> <tel:617-724-2358>>> >> <tel:617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> <tel: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>> >> <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>> >> >> <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> >> 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> >> >> 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>> >> <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 >> >> >> 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> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto: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>> >> <tel: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>> <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> >> 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> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> -- 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/ >> >> >> >> -- 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
