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FSL  February 2008

FSL February 2008

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Subject:

Re: Reply if you use FSL's flirt to affine register your images

From:

Tom Johnstone <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 4 Feb 2008 15:58:02 +0000

Content-Type:

text/plain

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text/plain (125 lines)

Hi Donna,

This reminds me of the reviewer comment I once got that block designs
were obsolete since event-related designs were now possible. Nonsense
of course.

Given i) the widespread use of affine transformations, ii) the fact
that since they warp low-resolution functional data to a blurry
average template, most studies aren't going to see any advantage in
nonlinear transformations, I think the justification for continued use
of affine transformations is at least as strong as for continued use
of average template-based analysis of group data. Now, the argument
can be (and has been) made that such average template methods are
deeply flawed, but somehow I don't think it would be reasonable for
such techniques to be banished overnight.

Just my 5p.

-Tom

On Feb 4, 2008 3:48 PM, Donna Dierker <[log in to unmask]> wrote:
> Steve and FSL users,
>
> I apologize for the fuss and confusion.  I certainly should have thought
> to ask users to reply to me rather than the list.  (I had forgotten that
> the list is configured to reply to the list, rather than to the poster.
> And I'm not recommending the list behavior be changed; I prefer it as it
> is.)
>
> The reviewer's comment was not about FSL flirt in particular; rather,
> he/she insinuated linear/affine volume-based registration (VBR) is
> obsolete (the context being ordinary fMRI analysis).  (If the reviewer
> is right, the paper under review is less relevant.)
>
> While I certainly agree that nonlinear VBR has advantages in many
> contexts, I don't think affine/linear VBR is irrelevant.  In fact, I
> believe affine VBR has distinct advantages over nonlinear methods in
> some contexts.  This reviewer is clearly a big nonlinear VBR fan, who
> needs to be reminded how widely used affine VBR is.  Steve's point is
> well-taken:  I don't need a reply count to make my point.
>
> Apologies again,
>
> Donna
>
>
> On 02/04/2008 09:24 AM, Martin M Monti wrote:
> > Steve, sorry to suggest differently, but given that it's highly likely
> > that most people on this list use FLIRT, wouldn't it be more
> > productive if she actually posted what the uncertainty is about?
> > Quite simply, if it is a reasonable criticism/request then almost
> > everybody will be interested in what the reviewer has to say, the more
> > considering the fact that we may get similar feedback in future reviews.
> >
> > Of course, if Donna feel it's a confidential matter -- perfectly
> > understandable -- or a not-too-reasonable comment, as it sometimes
> > happens, then never mind...
> >
> > just a suggestion though,
> >
> > all the best
> >
> > martin
> >
> > Steve Smith wrote:
> >> Hi - could I suggest that people email Donna Dierker directly, rather
> >> than generate too many emails in the inboxes of people on the list!
> >>
> >> Donna - not sure what the reviewers are asking about; FLIRT is
> >> certainly one of the most widely-used of the components in FSL. If
> >> you search in NeuroImage there's over 80 articles mentioning FLIRT,
> >> but I'm not sure if that's the kind of statistics that you're after.....
> >>
> >> Cheers, Steve.
> >>
> >>
> >>
> >> On 4 Feb 2008, at 15:00, David Gutman wrote:
> >>
> >>> I regularly "FLIRT" as well.
> >>>
> >>> DAG
> >>>
> >>>
> >>>
> >>> On Mon, Feb 4, 2008 at 9:42 AM, Donna Dierker
> >>> <[log in to unmask]> wrote:
> >>> I'm hoping to be inundated with replies, which will help me address a
> >>> reviewer comment.
> >>>
> >>> Donna Dierker
> >>> Van Essen Lab
> >>>
> >>>
> >>>
> >>> --
> >>> David A Gutman, M.D. Ph.D.
> >>> Department of Psychiatry & Behavioral Sciences
> >>> Emory University School of Medicine
> >>
> >>
> >> ---------------------------------------------------------------------------
> >>
> >> Stephen M. Smith, Professor of Biomedical Engineering
> >> Associate Director,  Oxford University FMRIB Centre
> >>
> >> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> >> +44 (0) 1865 222726  (fax 222717)
> >> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> >> ---------------------------------------------------------------------------
> >>
> >
>



-- 
School of Psychology and CLS
University of Reading
3 Earley Gate, Whiteknights
Reading RG6 6AL, UK
Ph.  +44 (0)118 378 7530
[log in to unmask]
http://www.personal.reading.ac.uk/~sxs07itj/index.html
http://beclab.org.uk/

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