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@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@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, stdp82@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@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, stdp82@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@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, stdp82@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:
- 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
- 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@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, stdp82@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@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, stdp82@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 >>> greve@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 > greve@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 greve@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
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@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@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@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, stdp82@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@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, stdp82@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@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, stdp82@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@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, stdp82@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@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, stdp82@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 >>>> greve@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 >> greve@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 greve@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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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
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@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@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@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@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, stdp82@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@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, stdp82@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@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, stdp82@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@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, stdp82@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@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, stdp82@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 >>>> greve@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 >> greve@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 greve@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
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@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@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@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@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@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, stdp82@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@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, stdp82@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@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, stdp82@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@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, stdp82@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@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, stdp82@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 >>>>> greve@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 >>> greve@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 > greve@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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
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