Hi - in general all these combinations of generating and applying
transformations are straightforward with the flirt and convert_xfm
utilities. I'm not sure though why you are wanting to resample the
FMRI data outside of FEAT? Will FEAT not do what you want in the
normal ways and take care of the resampling of the data for higher-
level analyses?
Cheers.
On 29 Aug 2007, at 13:56, N.M. van Strien wrote:
> Dear FSL experts,
>
> I have a question about the registration of a very limited fov
> functional
> dataset to standard space. I can register the dataset to standard
> space, but
> not in a three step approach, as can be set up with the feat GUI.
> Instead I
> use FLIRT with the following steps:
>
> Part 1 register structural datasets to standard space.
> # A) t2_mean (initial hi-res image)-> t2_sag_brain (hi-res image)->
> t1_brain
> (this is all intra-individual)
> # B) t1_brain -> MNI152_T1_1mm_brain
> # C) t2_mean -> MNI152_T1_1mm_brain (initial hi-res image -> to
> standard)
>
> Part 2 apply the obtained transformation to the functional data.
> # D) Resample functional data to the same resolution of the t2_mean
> image
> (the functional and the t2_mean had the exact scan orientation, so no
> additional registration is needed)
> # E) Resampled_functional -> t1_brain
> # F) Resampled_functional2t1_brain -> MNI152_T1_1mm_brain
>
> My first question is, how to apply this transformation to my first
> level
> (filtered_func) data, so that I can use it in the higher level
> analysis?
> Which transformation matrices do I need to place where, so that the
> higher
> level feat will be able to use it?
> My second question is if step E and F can be combined by
> concatenating the
> transformation matrices? I tried this, but ended up having a very
> different
> result then when using E and F as seperate steps. Would there be a
> way (to
> use convert_xfm) to get the proper transformation in one step?
>
> Thank you,
>
> Niels van Strien
> VU university medical center
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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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