Hi Naama,
yes you're right, in this case, this is better to run tbss3 with the -S option...
Cheers,
Gwenaëlle
--- En date de : Mar 21.4.09, Naama Barnea-Goraly <[log in to unmask]> a écrit :
> De: Naama Barnea-Goraly <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] Is this a valid thing to do? ( 3 groups tbss comparison)
> À: [log in to unmask]
> Date: Mardi 21 Avril 2009, 18h36
> Thanks Gwenaelle,
>
> This is a pediatric sample, so I assume it is better to run
> with the -S option ? Not a problem, I already ran it and the
> skeletons are all the same now, was just checking ;-)
>
> Best,
>
> Naama
>
> On Apr 21, 2009, at 9:23 AM, Gwenaëlle DOUAUD wrote:
>
> > Hi Naama,
> >
> > yes, it would be valid, but I presume you don't
> need to rerun the whole 2-4 steps...
> > It looks slightly "misregistered" quite
> likely because you ran tbss3 with the -S option, so the mean
> FA and skeleton are derived for each of your group. The
> skeletons are different, but the registration should be the
> same if you have run the tbss2 step with the FMRIB58
> template.
> > If so, then you don't need to run it again. You
> just need to run the tbss3 with the option -T with all your
> subjects in the same FA directory, then tbss4. Basically
> what you want here is a common skeleton in order to be able
> to compare each group.
> >
> > Cheers,
> > Gwenaëlle
> >
> >
> > --- En date de : Mar 21.4.09, Naama Barnea-Goraly
> <[log in to unmask]> a écrit :
> >
> >> De: Naama Barnea-Goraly
> <[log in to unmask]>
> >> Objet: [FSL] Is this a valid thing to do? ( 3
> groups tbss comparison)
> >> À: [log in to unmask]
> >> Date: Mardi 21 Avril 2009, 17h48
> >> I have 3 groups: subjects, relatives and controls.
> We ran
> >> separate t-tests to get our results, but now I
> would like to
> >> show them on one image and when I overlay them
> they are
> >> slightly "misregistered". I am assuming
> this is
> >> because the registration is a little different in
> each
> >> comparison. I would also like to extract the
> values from
> >> regions of significant between group differences.
> >>
> >> Is it valid to run tbss_2- tbss_4 on all subjects
> (all 3
> >> groups together) and then fslsplit/fslroi the
> groups that I
> >> want, run analysis, generate images and extract
> values for
> >> graphs?
> >>
> >> Thanks,
> >>
> >> Naama
> >>
> >>
> >>
> >> Naama Barnea-Goraly M.D.
> >> Instructor
> >> Center for Interdisciplinary Brain Sciences
> Research
> >> Stanford University Division of Child and
> Adolescent
> >> Psychiatry
> >> 401 Quarry Rd. MC 5795
> >> Stanford University School of Medicine
> >> Stanford, CA 94305-5795
> >> Phone: (650) 736-1874, fax: (650) 724-4794
> >>
> >>
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> >
>
> Naama Barnea-Goraly M.D.
> Instructor
> Center for Interdisciplinary Brain Sciences Research
> Stanford University Division of Child and Adolescent
> Psychiatry
> 401 Quarry Rd. MC 5795
> Stanford University School of Medicine
> Stanford, CA 94305-5795
> Phone: (650) 736-1874, fax: (650) 724-4794
>
>
> CONFIDENTIALITY NOTICE: This e-mail communication and any
> attachments may contain confidential information for the use
> of the designated recipients named above. If you are not
> the intended recipient, you are hereby notified that you
> have received this communication in error and that any
> review, disclosure, dissemination, distribution or copying
> of it or its contents is prohibited. If you have received
> this communication in error, please notify Stanford Medical
> Center immediately by telephone at (650) 725-5722 and
> destroy all copies of this communication and any
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