Dear Douglas, Thank you for your reply. I read the related FDR paper given in the “mri_fdr –help”.
Please tell me if the FDR correction in FreeSurfer do like the below. For the V vertices being tested, the general procedure is as follows: (1) Select a desired FDR bound q between 0 and 1. This is the maximum FDR that the researcher is willing to tolerate on average and we select q=0.05. (2) Order the P values from smallest to largest: P(1) ≤P(2) ≤• •≤P(v). Let v(i) be the vertex corresponding to P value P(i). (3) Let r be the largest i for which: P(i) ≤i/V*q/c(V), where c(V) is a predetermined constant. (4) Declare the voxels v(1), . . . ,v(r) active, or in other words, threshold the image of test statistics at the value corresponding to the P value P(r). If I response like this, is it right? Thank you very much, and looking forward to reply. Kind regards, Livia 2018-04-18 0:41 GMT+08:00 Douglas Greve <dgr...@mgh.harvard.edu>: > You should read the FDR paper for more detail. But the FDR is the number > of false positives relative to the total number of positives. The way it is > interpreted is that when you look at an image, 5% of the voxels above > threshold are false. You don't know which 5%. If the 5% came out of a big > blob, probably you would not change your conclusion about that blob. If > there were a few single voxels that were above threshold, you probably > don't want to write your paper around it. > > On 4/16/18 11:42 PM, Livia Liu wrote: > > Dear Douglas, > > > Thank you for your reply. I run “mri_fdr –help” to get docs that include > some information for how to use this command. However, I still don’t know > how FDR was used to correct for multiple comparisons. > > > This question is an opinion given by one reviewer, and I really don’t know > how to reply. > > For the description "To correct for multiple comparisons, the thresholds > of the P maps were set to yield an expected false discovery rate (FDR) of > 0.05." The reviewer said “Would help to provide more details as to how FDR > was used to correct for multiple?” > > > Would you please give me some help to response the question? Thank you > very much. > > > Kind regards, > > Livia > > 2018-04-17 0:40 GMT+08:00 Douglas N. Greve <dgr...@mgh.harvard.edu>: > >> You can also use mri_fdr Run it with --help to get docs >> >> >> On 04/16/2018 10:23 AM, Livia Liu wrote: >> > >> > Dear FS experts, >> > >> > I'd like to know that how FDR was used to correct for multiple >> > comparisons. I do FDR correction in two way in FreeSurfer. >> > >> > 1, Do the FDR correction in the qdec tool. And the page of “False >> > Discovery Rate” in the page “Multiple-Comparisons Correction in Qdec” >> > was lost. >> > >> > 2, Use “lme_mass_FDR.m” to do the FDR correction in LME model, which >> > was based on Tom's FDR.m in the github, however the page was also lost. >> > >> > Would help to provide more details as to how FDR in the two way was >> > used to correct for multiple comparisons? >> > >> > >> > Thank you very much, and looking forward to reply. >> > >> > Kind regards, >> > >> > Livia >> > >> > >> > >> > >> > _______________________________________________ >> > 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 . 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 > listfreesur...@nmr.mgh.harvard.eduhttps://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 . 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. > >
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