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 > 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>> 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>>> 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>>>> 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>>> >> >> > >> 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>>> >> 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/ >> >> _______________________________________________ >> 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>>> >> >> 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>> >> 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/ > >
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