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
