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Hi Luke, Yes, that's correct. All the best, Anderson On Mon, 19 Aug 2019 at 07:10, Luke Baxter <[log in to unmask]> wrote: > Hi Anderson, > > > > OK, I think I get this. Since I have a single modality, there is no need > to include modality-related flags (don’t use -npcmod or -corrmod). And the > overall effect of me including six designs ( six -d flags) and one > t-contrast (one -t flag, containing “+1 /n -1”) results in a pooled net > total of 12 contrasts. So I just need to include flags for > testing/correcting/pooling over contrasts. The -npccon flag will do the > joint inference over the 12 contrasts for my global null hypothesis test. > And the -corrcon flag will do the corrections for multiple testing for each > of my partial tests. > > > > Pretty sure I’ve got that correct, but just let me know if that’s still > off. Thank you very much, Anderson – this has been super helpful. > > > > All the best, > > Luke. > > > > *From: *FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > "Anderson M. Winkler" <[log in to unmask]> > *Reply to: *FSL - FMRIB's Software Library <[log in to unmask]> > *Date: *Friday, 16 August 2019 at 13:42 > *To: *"[log in to unmask]" <[log in to unmask]> > *Subject: *Re: [FSL] PALM NPC query - 1 modality, 2 contrasts, and 6 > designs > > > > Hi Luke, > > > > I'm sorry -- in the first post, it's -npccon that you need, not -npcmod. > The -npccon will do the joint inference over the 12 contrasts, therefore > pooling together all the 6 designs. > > > > There isn't a -corrdes or -npcdes option... combination and correction > happen at the level of the input data, or of the hypotheses tested on that > data; the latter are specified by the contrasts. The combination of designs > is the combination of contrasts, in that it's the former that indicate how > the latter are meant to be tested. > > > > So it seems to me that all that you need is replace -corrmod for -corrcon > and you should be ready to go. > > > > All the best, > > > > Anderson > > > > > > On Thu, 15 Aug 2019 at 13:12, Luke Baxter <[log in to unmask]> > wrote: > > In short(er): > > There is an "-npcmod" flag to enable NPC over modalities. > There is an "-npccon" flag to enable NPC over contrasts. > Is there an equivalent of an "-npcdes" flag to enable NPC over designs? > > Since I have multiple contrasts and multiple designs, ideally I would use > something like "-npccon" and "-npcdes". I presume "-npcmod" would do > nothing in my case, since I only have a single modality. That is, I only > have one -i input, and multiple -d inputs, and my -t input csv file has two > rows (two contrasts). > > The wiki says/implies I can do NPC over designs, but I can't see the > appropriate flag. And as I mentioned in the last post, I can't see the > relevant outputs from PALM. > > To labor the point, correcting over modalities produces an mfwep file, > correcting over contrasts produces a cfwep file, and correcting over both > gives an mcfwep file. If correcting over designs (using the hypothetical > -npcdes flag) produced a dfwep file, I believe I'm looking for something > like a dcfwep file. For each partial test. > > I'd also like the NPC global null (across contrasts and designs) > equivalent to combining all designs into one and doing a global f-test. > > Many thanks, > Luke. > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1