Hi Steve,
Thanks for replying.
I tried lowering the warp resolution to 8mm, but the registration did not really improve.
How far can I go in lowering the warp resolution? Are they any other processing steps that I should try in order to improve the registration.
The preprocessing already includes a fieldmap unwarping.
Cheers,
Annouchka
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Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Stephen Smith [[log in to unmask]]
Verzonden: vrijdag 12 augustus 2011 8:31
Aan: [log in to unmask]
Onderwerp: Re: [FSL] FEAT initial_highres2highres
Hi - if the problems are just around the ventricles, the issue is likely to be with the nonlinear registration, not the initial affine? Is the overall registration (globally) between functional and structural reasonable? If you have huge atrophy in some subjects then maybe you need to increase the detail of the nonlinear registration - so maybe reduce the warp resolution spacing?
Cheers.
On 11 Aug 2011, at 11:10, Annouchka Van Impe wrote:
Dear all,
I'm using Feat to analyze 2 sets of fMRI data: an elderly group and a young control group. I'm having problems with registering the data to MNI space, especially in the elderly group. The alignment around the ventricles is not so good. I'm using the following settings in the FEAT GUI:
-Initial structural image: a whole brain-extracted epi scan (Normal search, 3DOF)
-Main structural image: brain-extracted T1 (Normal search, 6DOF)
-Standard space: MNI152_T1_1mm_brain (Normal search, 12 DOF, non-linear, warp resolution 10 mm)
The problem seems to arise when registering the initial highres to the main structural image (registration of the main structural image to standard space is fine). I' ve tried changing the DOFs and changing the settings from 'normal search' to 'full search' but nothing seems to help much.
Any suggestions on how to improve this registration would be greatly appreciated.
Kind regards,
Annouchka
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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]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve
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