Freesurfer

freesurfer@nmr.mgh.harvard.edu

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R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 12 Oct '17

12 Oct '17

I have applied the contrasts that we discussed in the previous mails but they produce doubt results. In summary, I aim to look at: A- Difference between groups without considerer the covariate effect (I suppose that the maps will be in the intercept folder) ---> ANOVA between 4 groups B- Clusters in which the fMRI (dependent variable) is associated to the structural data (covariate), taking in account the groups (I suppose that the maps will be in the slope folder) ---> MANOVA between 4 groups Please could you check the contrast reported below? I suspect that there are some errors because, looking at results: The slope map is the inverse in color of the intercept map and the intercept did not correspond to the results which I obtain by using G4V0 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 0.25 0.25 0.25 0.25 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25 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 Best regards Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 11-ott-2017 17.28 >A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance > >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, stdp82(a)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 <greve(a)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, stdp82(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>> Data: 9-ott-2017 22.56 >>>> A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>> Data: 3-ott-2017 16.19 >>>>>> A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> Data: 2-ott-2017 16.58 >>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 10/01/2017 05:08 PM, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>> Data: 5-set-2017 22.59 >>>>>>>>>> A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>>>>> A: <freesurfer(a)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, stdp82(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>> -- >>>>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>>>> MGH-NMR Center >>>>>>>>>>>> greve(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> greve(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)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(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)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(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 12 Oct '17

12 Oct '17

I have applied the contrasts that we discussed in the previous mails but they produce doubt results. In summary, I aim to look at: A- Difference between groups without considerer the covariate effect (I suppose that the maps will be in the intercept folder) ---> ANOVA between 4 groups B- Clusters in which the fMRI (dependent variable) is associated to the structural data (covariate), taking in account the groups (I suppose that the maps will be in the slope folder) ---> MANOVA between 4 groups Please could you check the contrast reported below? I suspect that there are some errors because, looking at results: 1- The slope map is the inverse in color of the intercept map. 2- Newly, I would to verify whether the fcMRI difference observed between groups are associated to change in covariate (volume). 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 0.25 0.25 0.25 0.25 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25 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 Best regards Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 11-ott-2017 17.28 >A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance > >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, stdp82(a)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 <greve(a)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, stdp82(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>> Data: 9-ott-2017 22.56 >>>> A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>> Data: 3-ott-2017 16.19 >>>>>> A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> Data: 2-ott-2017 16.58 >>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 10/01/2017 05:08 PM, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>> Data: 5-set-2017 22.59 >>>>>>>>>> A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>>>>> A: <freesurfer(a)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, stdp82(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>> -- >>>>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>>>> MGH-NMR Center >>>>>>>>>>>> greve(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> greve(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)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(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)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(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

volume vs surface-based and surface smoothing
by Alissa Stafford 12 Oct '17

12 Oct '17

Hello, I am trying to understand the preprocessing functions to successfully complete surface-based analysis. I am confused about what is happening on the volume level and when exactly the surface is being created. My questions revolve around register-sess and rawfunc2surf-sess. Registration has 2 parts: 1: the native anatomical space is registered with the fsaverage space. This is happening during recon-all. 2: native functional data is registered with the native anatomical data. This is happening during register-sess in preprocess-sess. Aren’t these both volume-based registrations? If not when are the surfaces created? My concern is that it is volume-based and I was under the impression from this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all registrations should be done on the surface. I am also confused about rawfunc2surf-sess. I believe up until this function in preprocess-sess, everything has been done in the volume so this is the first step that is done in the surface, is that correct? And then does this do smoothing? I realized it has a fwhm input option so it must smooth. So is this where the functional data is now expressed in the surface and it also smooths? Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess? I basically just want to be making sure I understand when registration is volume-based or surface-based and when it’s appropriate to use volume-based. And I was using the rawfunc2surf function assuming it was for smoothing, but I am not so sure if this only creates the surface or also smooths. Thanks, Alissa

1 0

Postdoc position studying MRI measures following vision loss
by Visscher, Kristina M 12 Oct '17

12 Oct '17

A postdoctoral scholar position is available to work on a project using functional and structural MRI to assess how connectivity of visual areas is altered following loss of central vision and increased use of peripheral vision in the Visscher lab at the University of Alabama at Birmingham (https://labs.uab.edu/visscher/) This project is part of the NIH-funded Human Connectome Project, Connectomes in Human Diseases program. Applicants must be motivated and have prior experience with programming and imaging data analysis. Prior work in computational methods, vision, psychophysics, and/or eye tracking is a plus. Please send cover letter detailing your interests and fit with the lab, CV, and contact information for 3 references by email to Kristina Visscher kmv(a)uab.edu<mailto:kmv@uab.edu>. UAB consistently ranks as one of the top locations among US universities for training postdoctoral scholars. Located in Birmingham, Alabama, a metro area of over a million people, where access to technical resources and a collaborative, supportive environment combine to make a strong environment for postdoctoral work, and a very reasonable cost of living makes life on a postdoc salary comfortable. You will have resources and collaborative opportunities from our Civitan International Neuroimaging Lab including our 3T Siemens Prisma scanner, the UAB Center for Low Vision Rehabilitation, the Comprehensive Neuroscience Center, the Alabama Advanced Imaging Consortium, and Auburn University's 7T MRI machine, among other resources. More information about these resources are at https://labs.uab.edu/visscher/resources. Kristina Visscher, Ph.D UAB Neurobiology Department kmv(a)uab.edu<mailto:kmv@uab.edu> | https://labs.uab.edu/visscher/

1 0

Extracting values via mri_segstats from middle of the cortex
by Yash Patel 11 Oct '17

11 Oct '17

Hi, I have a MT and T1W volume (processed through recon-all). I would like to extract all MT values that lie in the middle surface of the cortex, and run that through mri_segstats so I get average MT values for each cortical region in the DK-atlas. My workflow is as follows: 1. mri_vol2suf --mov <MT_vol> --hemi lh --projfrac 0.5 -- regheader <id> --reg <MT_reg_to_T1W.dat> --o <vol2surf.output.mgh> --interp nearest 2. mri_surf2vol --surfval <vol2surf.output.mgh> --hemi lh --fillribbon --identity <id> --template <T1W> --o <surf2vol.output.mgh. 3. mri_segstats --seg <aparc+aseg for subid.mgz> --i <surf2vol.output.mgh> --ctab --id <list of regions> --o <output.stats> Is this the correct way of going about it? I was wonder if its alright to use mri_vol2surf to get MT values on a T1W surface, and then mri_surf2vol to get the output from vol2surf into a T1W cortical ribbon. And finally run mri_segstats on the output of mri_surf2vol using the aprac+aseg for that subject. Thank you, Yash RRI, Baycrest Health Sciences University of Toronto

1 1

UMN Informatics Institute - Neuroimaging Staff Scientist posting
by bryon mueller 11 Oct '17

11 Oct '17

The University of Minnesota Informatics Institute (UMII) <https://research.umn.edu/units/umii> seeks a skilled, staff scientist to serve the MR Neuroimaging research community at the University of Minnesota. The successful candidate is expected to: (1) carry out consultations with researchers across the University and serve in the role of a staff scientist who provides technical assistance across multiple research groups; (2) provide technical and analytic support in designing and supporting neuroimaging analysis pipelines that will be run on platforms of the Minnesota Supercomputing Institute (MSI); (3) appropriately document work so that researchers are able to prepare grants, research papers and reports based on the analysis; (4) simultaneously support different versions of analysis tools that might require different libraries and operating system versions; (5) develop new computational environments, such as Docker, for major neuroimaging analysis platforms (AFNI, FSL, etc.) in the HPC environment at MSI; and (6) build computational workflows that scale and work across a broad range of file system storage. The successful candidate will join a growing group of imaging analysts in the University of Minnesota Informatics Institute. The Imaging Informatics Manager at the University of Minnesota Informatics Institute will serve as the supervisor. On a daily basis, the analyst will work closely with MR neuroimaging researchers, and staff at the Minnesota Supercomputing Institute. This position is both posted as a Researcher 5 <https://z.umn.edu/umii-neuroimaging-job-5>, Research Scientist (minimum required qualification: PhD) under Job Opening 319904 <https://z.umn.edu/umii-neuroimaging-job-5> (https://z.umn.edu/umii-neuroi maging-job-5) and as a Researcher 3 <https://z.umn.edu/umii-neuroimaging-job-3>, Assistant Scientist, (minimum required qualification: Bachelor's degree) under Job Opening 319899 <https://z.umn.edu/umii-neuroimaging-job-3> (https://z.umn.edu/umii-neuroi maging-job-3). Qualifications Required: • Background in scientific image processing, analysis or multi-dimensional signal processing • Have proficiency in at least one programming language (Python, MATLAB, Java, C++, …) • Be familiar with the Linux operating system • Have excellent interpersonal and organizational skills • Be able to articulate processes verbally and in writing • Be highly motivated to learn new technical skills Additional requirements for the Researcher 5 position (Job Opening 319904): • Doctoral degree in a science or engineering field • Experience in MR neuroimaging image analysis (fMRI, DWI, or structural) • Significant research experience and ability to work independently • Experience working in a team environment with people with diverse expertise • Publications, software, or grant applications demonstrating creativity and independence Preferred: • (for Researcher 3 position) Master’s degree in a science or engineering field • (for Researcher 3 position) Experience in MR neuroimaging image analysis (fMRI, DWI, structural) • (for both positions) Experience in medical image analysis • (for both positions) Experience with container technology, such as Docker • (for both positions) Experience in HPC environments • (for both positions) Experience with neuroimaging analysis software packages such as FSL, AFNI, SPM • (for both positions) Experience working in a team environment with people with diverse expertise

1 0

Overlap between Yeo networks and aparc2009 segments
by shahin＠nmr.mgh.harvard.edu 11 Oct '17

11 Oct '17

Dear Experts, We are looking for a way to measure the amount of overlap between each 'aparc 2009 segment' vs. 'Yeo 7 networks segments'. Currently I can do that by converting segments to labels and and then measuring the number of common vertices between them. But I was wondering if there is a more direct way to do it. Regards

2 1

R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 11 Oct '17

11 Oct '17

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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >Data: 9-ott-2017 22.56 >A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>> Data: 3-ott-2017 16.19 >>> A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>> Data: 2-ott-2017 16.58 >>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>> >>>>> >>>>> >>>>> On 10/01/2017 05:08 PM, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>>> Data: 5-set-2017 22.59 >>>>>>> A: <freesurfer(a)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, stdp82(a)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" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>> A: <freesurfer(a)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, stdp82(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> -- >>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>> MGH-NMR Center >>>>>>>>> greve(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve(a)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(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)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(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 3

How to calculate WM lobar volumes
by Shatil, Anwar Shahadat 11 Oct '17

11 Oct '17

Dear All: I want to find the WM lobar volumes in a set of MS patients. I also have the processed images from freesurfer. To extract the lobar volumes I used below codes from one of the previous threads of Freesurfer (https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-April/023232.h…) 1. mri_annotation2label --s <sub1> --hemi rh --lobesStrict lobesfile 2. mri_aparc2aseg —s <sub1> --labelwm --annot lobesfile 3. mri_segstats --seg mri/lobesfile+aseg.mgz --sum wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject <sub1> --surf-wm-vol --ctab /Applications/freesurfer/WMParcStatsLUT.txt —etiv Now, I don’t know how to get the volumes or which LUT table to use in the overlay. Please correct me if I used the correct LUT file in --ctab. Your guidance would be highly appreciated. Thanks, Anwar This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Obtaining an old-style license or running old FreeSurfer without it
by Mike Schmidt 11 Oct '17

11 Oct '17

I am re-running some MRI scans with multiple versions of FreeSurfer. I am aware that FreeSurfer 5.2.0 is deprecated and don't intend to use its output, other than for comparisons with current versions. My problem is that I have copied a .license file (as mikeschmidt(a)schmidtgracen.com from February 2017) that works successfully with version 6.0.0 (known-good) into FreeSurfer 5.2.0's FREESURFER_HOME and FreeSurfer 5.2.0 finds the file, but says it is invalid. Renaming the .license file to license.txt resulted in it not being found at all. I've even retrieved an old license file (as mschmidt(a)umc.edu from prior to April 2015) from backup that I used to use (email address no longer exists), thinking I had used it with 5.2.0 in the past, but it is also reported as invalid. I've read in the forum that 6.0.0 uses a different license file format due to libcrypt changes. But I can't seem to get new or old licenses to work. Is it possible to register for a replacement old-style license? Or is there another way to get 5.2.0 to work? I applied for a new license today to test everything before asking for help, expecting it would work with v6.0.0 but not 5.2.0. Testing validated my assumption, leading me to believe I need to acquire a valid license in the old format in order to run FreeSurfer version 5.2.0. Is that possible? Thank you for any assistance, Mike Schmidt

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