Hi,
It sounds like you're not quite following exactly what FEAT needs
here, possibly.
You should have non-betted AND betted structurals in the same
directory, for example
/Users/kent/sub1_struc.nii.gz
AND
/Users/kent/sub1_struc_brain.nii.gz
And it is the betted version that you should input into the GUI (/
Users/kent/sub1_struc_brain.nii.gz); FEAT will then automatically look
for the non-betted version for use in the FNIRTing.
Cheers.
On 28 Nov 2008, at 21:22, Kent Conover wrote:
> Hi,
>
> I am having difficulty using the FNIRT option in FEAT. I
> understand that
> non-linear registration requires two anatomical/structural files.
> FNIRT
> requires an initial affine registration based on a brain extracted
> anatomical image as provided by FLIRT. In addition FNIRT also
> requires a
> whole head image from which to derive the non-linear transformation.
> These
> two requirements currently one of trigger two errors, either a non-
> linear
> registration error (shrunken functional syndrome), or a linear
> registration
> error (homunculous head projected onto MNI standard syndrome). My
> problem
> stems from difficulty in providing both files. If I specify the brain
> extracted image to be the "Main structural image", then a warning
> window
> informs me that a "whole-head" image cannot be found, and that the
> non-linear registration will be suboptimal. This warning appears
> despite the
> presence of a single whole-head file with the suffix "_brain", (as
> per the
> instruction in the warning message), in the same directory as the
> "betted"
> anatomical. On the other hand, if an non-extracted anatomical image is
> specified to be the "Main structural image", then the linear
> registration fails.
>
> I have had success applying the non-linear warp files to the
> anatomicals
> via "applywarp", although I have yet to successfully warp functional
> files.
>
> I will appreciate any guidance, as I am eager to see what FNIRT
> can do!
>
> Regards,
>
> Kent Conover, Ph.D.
> Concordia University,
> Montreal, Quebec,
> Canada
>
---------------------------------------------------------------------------
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
---------------------------------------------------------------------------
|