Thanks In which contrast I must change "1" with "0.25"? What is the rationale to use 0.25?
Sent from Virgilio Mobile ________________________________ Il 10/10/2017, Douglas N Greve <gr...@nmr.mgh.harvard.edu> ha scritto: I don't understand what you mean by "where I should use" I thought I looked through all those contrasts a few weeks ago, no? On 10/10/2017 04:22 AM, std...@virgilio.it wrote: > You have suggested to use > 0 0 0 0 .25 .25 .25 .25 > to look the map where, considering the group differences, the covariate > predicts the dependent variable (functional connectivity) in 4GV1. > > Below I'm reporting the contrast that I have used. > Please could you check it and suggest correction? > Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please? > > Thanks > > C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 > C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 > C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 > C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 > C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 > C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 > C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 > C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 > C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 > C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 > C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 > C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 > C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 > C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 > C15) group.effect.intercept > 1 -1 0 0 0 0 0 0 > 1 0 -1 0 0 0 0 0 > 1 0 0 -1 0 0 0 0 > C16) group.effect.slope >> 0 0 0 0 1 -1 0 0 >> 0 0 0 0 1 0 -1 0 >> 0 0 0 0 1 0 0 -1 > > > > > > > > On 10/6/17 9:24 AM, std...@virgilio.it wrote: >> Thank you very much. >> Where I should put 0 0 0 0 .25 .25 .25 .25? >> Which are the contrast reported below that I should modify? >> >> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >> C15) group.effect.intercept >> 1 -1 0 0 0 0 0 0 >> 1 0 -1 0 0 0 0 0 >> 1 0 0 -1 0 0 0 0 >> C16) group.effect.slope >> 0 0 0 0 1 -1 0 0 >> 0 0 0 0 1 0 -1 0 >> 0 0 0 0 1 0 0 -1 > >> ----Messaggio originale---- >> Da: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> >> Data: 9-ott-2017 22.56 >> A: <freesurfer@nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance >> >> I don't know what you are asking >> >> >> On 10/6/17 9:24 AM, std...@virgilio.it wrote: >>> Thank you very much. >>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>> Which are the contrast reported below that I should modify? >>> >>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>> C15) group.effect.intercept >>> 1 -1 0 0 0 0 0 0 >>> 1 0 -1 0 0 0 0 0 >>> 1 0 0 -1 0 0 0 0 >>> C16) group.effect.slope >>> 0 0 0 0 1 -1 0 0 >>> 0 0 0 0 1 0 -1 0 >>> 0 0 0 0 1 0 0 -1 >>> >>> >>>> ----Messaggio originale---- >>>> Da: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> >>>> Data: 3-ott-2017 16.19 >>>> A: <freesurfer@nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance >>>> >>>> probably you want 0 0 0 0 .25 .25 .25 .25 >>>> >>>> >>>> >>>> On 10/3/17 10:10 AM, std...@virgilio.it wrote: >>>>> Many thank for your response. >>>>> Claryfing my question on point 3, >>>>> When I look in group.effect.slope, the map show the group difference >>> removing >>>>> the effect of the covariate. >>>>> Conversely, I would to obtain the map reporting only the effect of >>> covariate >>>>> on dependent variable (functional connectivity). >>>>> Is possible to look on it? >>>>> Regards >>>>> Stefano >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>> Data: 2-ott-2017 16.58 >>>>>> A: <freesurfer@nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>>> >>>>>> >>>>>> >>>>>> On 10/01/2017 05:08 PM, std...@virgilio.it wrote: >>>>>>> Hi, >>>>>>> on 4 groups, 1 covariate (4GV1) >>>>>>> >>>>>>> I run mri_glmfit using the following .mtx >>>>>>> >>>>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0 >>>>>> should be >>>>>> >>>>>> 0 0 0 0 1 0 0 -1 >>>>>> >>>>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>>>> C15) group.effect.intercept >>>>>>> 1 -1 0 0 0 0 0 0 >>>>>>> 1 0 -1 0 0 0 0 0 >>>>>>> 1 0 0 -1 0 0 0 0 >>>>>>> C16) group.effect.slope >>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>> >>>>>>> Please: >>>>>>> 1) Could you check whether the all .mtx are complete and corrected, in >>>>>>> particular the gr1+gr2-vs-gr3+gr4.intercept and the gr1+gr2-vs-gr3+gr4. >>>>> slope? >>>>>> they look correct, except for the one i noted >>>>>>> 2) Could you explain the meaning of: >>>>>>> gr1+gr2-vs-gr3+gr4.slope - does the average slope of grp1 and grp2 > differ >>>>> from that of grp3 and 4 >>>>>>> gr1+gr2-vs-gr3+gr4.intercept - same >>>>>>> group.effect.slope - interaction between group and covariate >>>>>>> group.effect.intercept - is there an effect of group on the inercept >>>>>>> 3) Which is the contrast identifying the effect of covariate on group >>>>>>> differences? >>>>>> not sure what you mean >>>>>>> Thanks >>>>>>> >>>>>>> Best regards >>>>>>> >>>>>>> >>>>>>> Stefano >>>>>>> >>>>>>> >>>>>>> >>>>>>>> ----Messaggio originale---- >>>>>>>> Da: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>>>> Data: 5-set-2017 22.59 >>>>>>>> A: <freesurfer@nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] R: Re: Map of covariance >>>>>>>> >>>>>>>> you would need to create a contrast to look for the interaction. If > you >>>>>>>> have four gruops and 1 covariate, then it would be >>>>>>>> >>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>> >>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>> >>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 09/05/2017 04:32 PM, std...@virgilio.it wrote: >>>>>>>>> Hi, >>>>>>>>> e.g., by considering two or more groups, I would like to map the >>> clusters >>>>>>>>> reporting the covariance between the functional connectivity or >>> cortical >>>>>>>>> thickness (dependent variable) and age, tacking in account the group >>>>>>>>> differences. >>>>>>>>> Instead, I'm not interested to map the group differences, taking in >>>>> account >>>>>>>>> the nuisance factors. >>>>>>>>> Thanks, >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>>> ----Messaggio originale---- >>>>>>>>>> Da: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>>> A: <freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> Ogg: Re: [Freesurfer] Map of covariance >>>>>>>>>> >>>>>>>>>> I don't understand what you are asking. can you elaborate? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 08/30/2017 12:50 PM, std...@virgilio.it wrote: >>>>>>>>>>> Hi list, >>>>>>>>>>> by applying a design e.g. 4GV1 in fsgd I could assess the > dependence >>>>>>>>>>> of group differences taking in account the effect of covariate. >>>>>>>>>>> Anyway, where I should look if I want assess the the map showing > the >>>>>>>>>>> clusters in which the dependent variable is associated to > covariate, >>>>>>>>>>> tacking in account the group difference? Please could you suggest > my >>>>>>>>>>> the path? >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> Stefano >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>> edu/transfer/outgoing/flat/greve/ >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. > edu/transfer/outgoing/flat/greve/ >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> >>>>>>> >>>>>> -- >>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> _______________________________________________ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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