HI - yes, it looks also possibly like the fieldmap and fieldmap mag
images are not in the same space with the same alignment and
orientation, and possibly are even entered into the GUI the wrong way
round?
Cheers.
On 26 Nov 2007, at 08:42, Timm Wetzel wrote:
> On 25.11.2007, at 00:14, gtau wrote:
>
>> Im writing to get some help with registration.
> [...]
>> I then deskulled and registered it to example func running the FEAT
>> GUI.
>> FEAT completed running but in the report, the registration is
>> really off.
>
> Your FEAT analysis is overlaying sagittal and coronal images (best
> seen in the second and second to last rows).
>
> I've seen a very similar effect with FLIRT, and it seems that in my
> case it was caused by unexpected orientation info in the NiFTI header.
>
> Does the FLIRT part of your processing complain about the input
> images having both qform and sform entries in the NiFTI header? (You
> might need to run it with `-v´.)
> If yes, I'd either try to use another NiFTI converter or add `-
> usesqform´ to the FLIRT command line.
>
> You can manually check the orientation info with fslhd; in my case
> FreeSurfer's mri_convert apparently generally fills both the qform
> and sform entries with the same data.
>
>
> Regards,
> Timm
---------------------------------------------------------------------------
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
---------------------------------------------------------------------------
|