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.
Natasha On Tue, Jan 28, 2014 at 12:11 PM, Douglas N Greve <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>> 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/ > >
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