Yes, that looks right. It is the basic FDR computation
On 04/18/2018 12:53 PM, Livia Liu wrote: > > 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 > <mailto: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 <mailto: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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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. 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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 > <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
