Hi Bruce, Jürgen and Chris Thank you for elaborating further. I've gone with a Bonferroni correction as I had a limited number of tests (a-priori hypothesis). But just out of interest Chris, you mentioned you found correlations between subcortical structures, do you have a reference I could look at? The tool that Jürgen suggested requires we enter a correlation coefficient, so I wondered if I could use published values or whether I'd need to calculate my own (if so, could you please recommend a way of doing that in Freesurfer or FSL?)
Many thanks in advance Kind regards Reem -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Jürgen Hänggi Sent: Sunday, 22 July 2012 7:47 p.m. To: Watson, Christopher Cc: Freesurfer Mailinglist Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC Hi Chris Yes there are such tools. Bonferroni oder Sidak test that take into account the correlated measures. Here you can find these tools http://www.quantitativeskills.com/sisa/calculations/bonfer.htm Cheers Jürgen On [DATE], "Watson, Christopher" <[ADDRESS]> wrote: > What about, for example, the correlations I've seen in a cohort of subjects. > > In 158 subjects aged 10-19 (both controls and patients), the > correlation between L & R thalamus is 0.91, and the correlations > between L & R of caudate, putamen, pallidum, hippocampus, and amygdala were > all 0.75 or higher. > > I would think that a Bonferroni correction would be incredibly > conservative and, in my opinion, just plain wrong because true > significant diff's would be missed. Is there any principled way of > dealing with multiple tests that are correlated? > > Thanks, > Chris > ________________________________________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Saturday, July 21, 2012 12:01 PM > To: Watson, Christopher > Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Questions about correction over 2 > hemispheres and MCC > > Hi Chris, > > bonferroni will be overly conservative in that case, but we rarely > really know the true covariance structure of the data, so we would > rather err on the side of being conservative. > > cheers > Bruce > On Fri, 20 Jul 2012, Watson, Christopher > wrote: > >> Hi Doug et al, >> >> The 2nd question is something I've wondered about. Doesn't a >> Bonferroni correction assume that the measures are independent? >> If so, I think in the case of subcortical structures, it is incorrect >> to use this method, as e.g. the putamen and pallidal volumes are not >> independent of one another. >> If not, and it is acceptable to use when there are dependencies >> between measures, how do you calculate the FWE? It wouldn't be equal >> to alpha/n, unless I am misunderstanding something. >> >> Thanks, >> Chris >> ________________________________________ >> 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: Friday, July 20, 2012 2:38 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Questions about correction over 2 >> hemispheres and MCC >> >> Hi Reem, it looks like you've done everything correctly (sorry for >> the null result). As for your second, question, I don't think there >> is a way other than Bonferroni. You can try FDR, but it makes the >> interpretation a little messy. >> doug >> >> On 07/19/2012 07:59 PM, Reem Jan wrote: >>> >>> Hi Doug >>> >>> I hope it?s okay that I double check I?m doing the correction over 2 >>> hemispheres correctly and ask a question regarding correction for >>> multiple comparisons. I will briefly describe what I have done: >>> >>> I have 2 groups of subjects ? Drug addicts (n= 17) and controls (n=20). >>> >>> 1.I ran a surface thickness study: >>> >>> ·For the ?mri_glmfit? command, I used DOSS and specified a contrast >>> of >>> +1 -1 0 (Controls > MA) >>> >>> ·I ran a pre-cached simulation with the following command: >>> mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos >>> >>> ·This simulation should only have corrected for the left hemisphere >>> as I understand it. My cluster summary text file showed me that a >>> cluster survived in the insula. I interpreted this as ?controls had >>> higher grey matter thickness in this cluster located in the insula >>> than drug addicts?. However, this was only corrected over the left >>> hemisphere (when I ran the same simulation in the right hemisphere, >>> nothing survived multiple comparison correction). >>> >>> ·I now wanted to correct the lh results for 2 hemispheres. From the >>> help menu of ?mri_glmfit-sim?, I understood you can do this in 2 >>> ways, are both of these correct and give the same result? >>> >>> a.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2 >>> spaces --no-sim csdbase >>> >>> b.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos >>> --cwpvalthresh 0.025 >>> >>> ØNo clusters survived the Bonferroni correction over both hemispheres. >>> So I assume I can no longer report this result? >>> >>> 2.I ran a subcortical volume study: >>> >>> ·I used SPSS to perform the statistical analysis on each of 14 >>> subcortical structures (left and right). Is there a good way to >>> correct for multiple comparisons, apart from Bonferroni, which would >>> be very conservative? >>> >>> Many thanks for your advice. >>> >>> Kind regards >>> >>> Reem >>> >>> *Reem Jan*** >>> >>> BPharm (Hons), RegPharmNZ >>> >>> PhD Student / Pharmacist >>> >>> School of Pharmacy, Faculty of Medical & Health Sciences, The >>> University of Auckland, Private Bag 92019, Auckland, New Zealand. >>> >>> Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138 >>> >>> F: +64 9 367 7192 >>> >>> *From:*freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of >>> *Douglas Greve >>> *Sent:* Friday, 20 July 2012 11:52 a.m. >>> *To:* freesurfer@nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] slice-by-slice predictors >>> >>> Sorry, not possible. >>> >>> On 7/19/12 6:56 PM, Caspar M. Schwiedrzik wrote: >>> >>> Hi! >>> Is it possible to have slice-by-slice predictors in Freesurfer, and >>> if so, how? >>> Thanks, >>> Caspar >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto: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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> _______________________________________________ >> 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 . 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. >> >> >> _______________________________________________ >> 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 ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. 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