Hi Kamila,
Indeed - it's hard to register these directly, due to a combination
of the quite different shaped brains (for example very different
ventricles) and the limited field-of-view. I've gotten reasonable
results by flipping front-back to be roughly aligned with the MNI152
and then turning the FLIRT search off, and aligning both images to
the MNI152.
avwswapdim SOURCE -x -y z SOURCEflip
flirt -in SOURCEflip -ref /usr/local/fsl/etc/standard/avg152T1_brain -
o SOURCEflip2std -nosearch
avwswapdim TARGET -x -y z TARGETflip
flirt -in TARGETflip -ref /usr/local/fsl/etc/standard/avg152T1_brain -
o TARGETflip2std -nosearch
Is that good enough do you think?
Cheers, Steve.
lovely goal.
On 30 Jun 2006, at 13:59, Kamila Szulc wrote:
> Dear Steve,
>
> Yes, I have tried all the options in the FSL registration tool and
> none of them worked. I will upload the images as you suggested.
>
> Thank you,
> Kamila
>
>
> On 6/30/06, Steve Smith <[log in to unmask]> wrote: Hi - have you
> tried varying the FLIRT search and DOF options? If you
> still can't make this work then feel free to upload an example input
> and reference image for us to have a look at:
>
> Please upload the files in a single compressed tarfile to
> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> and then email me the upload ID.
>
> Cheers, Steve.
>
>
>
> On 30 Jun 2006, at 12:47, Kamila Szulc wrote:
>
> > Dear FSLusers,
> >
> > I'm using FSL3.3 to register b0 images of different subjects to a
> > target b0 image acquired using the same parameters.
> >
> > The affine registration seemed to work quite well for most of the
> > subjects but I have 4 data sets that I'm not able to register to a
> > target image (I tried to register images with and without bet and
> > the registration still didn't work).
> >
> > If it would help I could attach some screenshots of the target
> > image and one of the object images (source) for which the
> > registration failed.
> >
> > I would very much appreciate if you could let me know if you have
> > any ideas as to why registration didn't work and if there is any
> > way to fix this problem.
> >
> > I look forward to hearing from you.
> >
> > Thank you,
> >
> > Kamila Szulc
> >
>
>
> ----------------------------------------------------------------------
> --
> ---
> 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
> ----------------------------------------------------------------------
> --
> ---
>
------------------------------------------------------------------------
---
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
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