Hi Paul,
yes, you should use a non-linear registration to register one subject to another one or to a template. However, you should not use *any* registration prior to segmentation but do it the other way round (as in the optimised VBM protocol), as segmentation does not accommodate well with interpolation.
Cheers,
Gwenaëlle
> De: Paul Renslow <[log in to unmask]>
> Objet: Re: [FSL] FNIRT vs FLIRT
> À: [log in to unmask]
> Date: Lundi 22 novembre 2010, 22h56
> Fair enough, so I have several
> subjects: each subject has 4 mprag images per mri session,
> there are 3 sessions per year and each subject has up to 7
> yrs worth of data,, so then are you saying that after the 4
> nifti images are averaged together one would then use FNIRT
> to a standard template rather than FLIRT prior to
> segmentation?
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On Behalf Of Matt Glasser
> Sent: Monday, November 22, 2010 2:45 PM
> To: [log in to unmask]
> Subject: Re: [FSL] FNIRT vs FLIRT
>
> You don't need to ask to ask, just ask.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On Behalf
> Of Paul Renslow
> Sent: Monday, November 22, 2010 4:39 PM
> To: [log in to unmask]
> Subject: Re: [FSL] FNIRT vs FLIRT
>
> Thanks for your prompt reply: can I ask you some more basic
> question(s)
> regarding segmentation?
> Paul
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On Behalf
> Of Mark Jenkinson
> Sent: Monday, November 22, 2010 2:14 PM
> To: [log in to unmask]
> Subject: Re: [FSL] FNIRT vs FLIRT
>
> Hi,
>
> FNIRT is for non-linear registration - typically between a
> structural image
> and a standard-space template image. FLIRT is for
> linear registration
> which is for within-subject registration, such as
> functional to structural.
> You also need to do a linear registration with FLIRT before
> doing one
> with FNIRT. Note that both FLIRT and FNIRT are run by
> the FEAT GUI
> when doing a functional analysis, and you do not need to
> run these
> separately. You can find more information about
> registration in the
> FSL course lecture and practical on registration.
>
> All the best,
> Mark
>
>
>
> On 22 Nov 2010, at 21:49, Paul R wrote:
>
> > Hi there, as i am new to fsl,, and i have looked thru
> the archive and the
> tutorial(s) can u provide an understanding of when does one
> use FNIRT versus
> FLIRT
> > Thank you.
> > paul
> >
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Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
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