the rational is to make them sum to 1.0 so that the gamma.mgh file has units of mm (or whatever the input units are). It is unimportant for p-values.
On 10/10/2017 01:54 PM, std...@virgilio.it wrote: > 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
