Great, thanks for your help Doug! Panos ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, June 03, 2013 2:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis Question
yes, I think so. Maybe others can comment. On 06/03/2013 02:49 PM, Fotiadis, Panagiotis wrote: > Ok, great, it seems in this case that even though the overlays in both cases > are very similar, the kurtosis in the second analysis (Diseased vs Controls > no gender taken under consideration) is slightly better. Therefore would it > be correct to assume that the second analysis is more trustworthy? > > Thanks, > Panos > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, June 03, 2013 2:34 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group Analysis Question > > yes > On 06/03/2013 02:26 PM, Fotiadis, Panagiotis wrote: >> I see. Would it be correct to say that better kurtosis would be illustrated >> as less significant clusters in the kurtosis.mgh overlay? >> >> Panos >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Monday, June 03, 2013 1:53 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Group Analysis Question >> >> Not necessarily. It could have been in the FS analysis. You can run >> mri_glmfit with --kurtosis (a hidden option). This will create a >> kurtosis.mgh and pkurtosis.mgh. Kurtosis is a measure of gaussianity of >> the residuals (larger being less gaussian). The pkurtosis the the sig >> (-log10(p)) of the probability of seeing the kurtosis under the null >> (ie, the residuals are gaussian). So you can see if one model gives you >> better kurtosis than another. >> >> doug >> >> >> On 06/03/2013 01:20 PM, Fotiadis, Panagiotis wrote: >>> I see. Yes from the one hand the results that I got make a lot more sense >>> in the second type of analysis, compared to the first one, however, there >>> are some somewhat important difference between the two analyses. If there >>> is an issue with the data, do you believe that it would be in the >>> acquisition? Because I checked the reconstructions and they look fine. >>> >>> Thanks, >>> Panos >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>> [gr...@nmr.mgh.harvard.edu] >>> Sent: Monday, June 03, 2013 11:24 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Group Analysis Question >>> >>> I would not expect them to be identical but similar. If they change a >>> lot there may be an issue with your data. >>> doug >>> >>> >>> >>> On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote: >>>> Hey Doug, >>>> >>>> I have run a group analysis on my data with two different ways. (The input >>>> is cortical thickness.) In the first analysis, I specified 4 groups >>>> (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas >>>> in the second, just two groups (Diseased, Healthy). One of the comparisons >>>> that I did was the age slope between Diseased and Healthy. Therefore in >>>> the first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 >>>> -0.5] and in the second analysis I set it to [0 0 1 -1]. However, the >>>> results that came up were somewhat different. For instance there were >>>> clusters in the second analysis that were significant but were not >>>> significant in the first analysis. >>>> Shouldn't the results be the same? >>>> >>>> Thank you, >>>> Panos >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> 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 >> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> 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 > 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 > > _______________________________________________ > Freesurfer mailing list > 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 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 _______________________________________________ Freesurfer mailing list 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 . 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