The cluster-forming threshold is needed to define what the clusters are. Once you have a cluster forming threshold, you get clusters with a certain size. Given the size, the FWHM, the cluster forming threshold, and the search space, a p-value for the cluster is computed.
On 01/28/2014 03:58 PM, harisnata...@gmail.com wrote: > 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/ >> > -- 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
