Hi - this all looks fine. It looks like the registrations are fine and the
small areas where the activation "leaves" the brain are probably due to a
combination of smoothing, and slight distortions between the EPI data and
the T1 structural.
You might get slightly better registration of the initial highres to the
main structural (the "main structural image" registration part of the GUI)
if you correct the initial highres with fieldmap correction, or, failing
that, use 12 DOF in this second stage of the registration.
Cheers.
On Fri, 21 May 2004, Jane Aspell wrote:
> Hi Steve
> I've put my feat directory of a first level feat analysis of one run on
> cayenne:
> /usr/fs5/aspell
>
> it's a tarred zipped directory called
> 2ndseries2.2.feat.tar.gz
>
> in it is also a folder called /highes_reg which contains the T1 image
> (struct.hdr) for the
> subject and a single stats image that i have registered to it with flirt -
> 2ndser2.2reg_shadowreg_cluster_mask_zstat1.hdr
>
> ...just to give you an example of what i mean.
>
> thanks again for the help
> jane
>
>
> In message <[log in to unmask]>
> FSL - FMRIB's Software Library <[log in to unmask]> writes:
> > Hi - no, FLIRT will have corrected for the different voxel sizes - if the
> > registration overlays look ok then any weird looking stuff in the
> > activation overlays can't be due to registration-related issues. It might
> > be worth you putting the full FEAT directory on a website so we can have a
> > look at the effects you are worried about.
> >
> > Cheers, Steve.
> >
> >
> > On Wed, 19 May 2004, Jane Aspell wrote:
> >
> > > Steve,
> > > some more points to add to the previous query...even though the
> > > registration page on the feat report looks ok my activations on highres
> > > overlay doesn't. i wondered if the problem might be a failure to match
> > > pixel sizes in the different images. for one subject both 24 slice
> > > functional EPI and 120 slice EPI ('initial sturctural') have pixdims
> > > 3,3,3 but for another subject the 120 slice is 4,4,3. i don't know why
> > > the latter is different for one of the subjects. could this difference
> > > between the 24 slice and 120 slice image for one of the subjects be
> > > causing a problem? and do i need to set some parameter (eg one of the
> > > advanced options) in flirt to allow for the fact that my 24 slice
> > > functional EPI (and 120 slice EPI) has slices at an oblique angle?
> > > thanks for your help
> > >
> > > Jane
> > >
> > >
> > >
> > > In message
> > > <[log in to unmask]> FSL
> > > - FMRIB's Software Library <[log in to unmask]> writes:
> > > > Hi - it's difficult to judge registration quality by looking at the
> > > > activation overlay - you should be clicking on the registration
> > > > evaluation image towards the bottom of the FEAT webpage report and
> > > > look at the detailed registration evaluation images - do they look ok?
> > > >
> > > >
> > > > Cheers, Steve.
> > > >
> > > >
> > > > On Mon, 17 May 2004, Jane Aspell wrote:
> > > >
> > > > > Hi
> > > > >
> > > > > I'm having some problems registering my functional data onto a highres
> > > > > image of an individual subject's brain. My functional data is in the
> > > > > form of 24 obliquely oriented slices mainly covering the occipital
> > > > > area (it's a vision study). The clusters of activation seem to 'flame
> > > > > out' from the brain in some areas, into 'space' by a few millimetres.
> > > > > This problem seems to be worse in occipital areas and not so bad in
> > > > > parietal areas. I have an idea that occipital areas are subject to
> > > > > more distortion than other areas - is this true? To register my
> > > > > functional to a highres with flirt i did a 7 parameter global rescale
> > > > > transformation from my 24 slice functional data to a 120 slice EPI
> > > > > (slices at the same angle as the functional) and another 7 param
> > > > > global rescale to my individual highres structural. is there anything
> > > > > you could advise i do to improve my registration?
> > > > >
> > > > > many thanks for your time,
> > > > >
> > > > > Jane Aspell
> > > > >
> > > >
> > > > Stephen M. Smith DPhil Associate Director, FMRIB and Analysis
> > > > Research Coordinator
> > > >
> > > > 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
> > > >
> > >
> > > --
> > > Dr Jane Aspell Department of Experimental Psychology, University of
> > > Oxford, South Parks Road, Oxford, OX1 3UD tel: +44 (0)1865-281606
> > >
> >
> > Stephen M. Smith DPhil
> > Associate Director, FMRIB and Analysis Research Coordinator
> >
> > 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
> >
>
> --
> Dr Jane Aspell
> Department of Experimental Psychology, University of Oxford,
> South Parks Road, Oxford, OX1 3UD
> tel: +44 (0)1865-281606
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
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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