Hi - the flirt binary update can be got from
http://www.fmrib.ox.ac.uk/fsldownloads/patches/1.3/
ttfn ;-)
On Mon, 4 Feb 2002, Marenco, Stefano (NIMH) wrote:
> FSL 1.3 and FLIRT 3.1 I thought these were the latest versions.
> But I think I saw a recent email on the list about FLIRT 4.1 (not described
> on the website). I cannot retrieve Steve's email on the buglet repair, what
> do I have to do?
> Stefano
>
>
> -----Original Message-----
> From: Mark Jenkinson [mailto:[log in to unmask]]
> Sent: Sunday, February 03, 2002 5:35 PM
> To: [log in to unmask]
> Subject: Re: [FSL]
>
>
> Dear Stefano,
>
> > I cannot do this in medx for two reasons: 1) the FSL utilities work only
> > with 3D registration; 2) even when I do the registration with air medx
> > cannot save a 2D transform, it can only save a 3D (that is really odd!!!,
> > and disappointing).
>
> Any 4x4 matrix where the third line and column are 0 0 1 0 is
> effectively a 2D transformation. This is the case for the ones
> you sent (up to a very tiny offset in z trans).
>
>
> > I tried to to 2D transforms in the flirt GUI, without changing cost
> > functions. I attempted first with my original images (t2 as reference, t1
> as
> > input). I got the message "child killed: SIGABRT", the output file was not
>
> OK, this is bad. You should *never* get SIGABRT or segmentation fault
> or anything like that, regardless of how horrible the images are.
> What version of FSL and FLIRT are you using?
> If it is an old version then it will not even support 2D registration.
> Otherwise you may need the latest buglet fix (see Steve's latest reply
> to the list regarding PET registration).
>
> > procedures. Should I try to apply the transforms to a 2D image and to a
> > reference volume from the command line?
>
> If you don't get errors in the command line version, then yes, you
> should use this. Just follow the procedure I outlined before.
> Apply the transformation (using -applyxfm -init) to either a single
> slice, using a single slice reference image, or to a 3D volume of
> slices, using an appropriate volume as the reference.
>
> Always remember that FLIRT uses the reference volume to determine
> the output FOV and voxel sizes. When using applyxfm mode this is
> the only use that the reference volume has, and the actual contents
> of the image are totally ignored.
>
> Hope this sorts everything out.
> All the best,
> Mark
>
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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