Hi - you need to verify that the structural to standard space
registration worked right in the first place! You need to do this
before trying to apply this transform to other (eg mask) images.
It also looks like your structural has not been BETted - see the FDT
manual for details on this. You may find that if your initial
structural's registration is still not working that you need to use
avwswapdim to reorient it.
Cheers, Steve.
On 5 Jun 2007, at 00:11, Dianne Patterson wrote:
> Dear group,
>
> Yet another newbie question:
>
> For post-bedpost registration of standard to structural images, is
> it important that the images are in the same orientation?
> (or just that fsl accurately understands the orientation of each
> image)
>
> Specifically,
> I have an spgr struct image that is collected sagittally...whereas
> the standard template image avg152T1 is axial...
> Registration produces *.mat files to convert between them,
> but now that I have been playing with flirt and masks for a while,
> I am wondering if there is a way to independently examine the
> registration success.
>
> Here's the result that caused me concern:
> >flirt -in frontal_lobe_L2.nii.gz -ref spgr.nii.gz -init
> standard2str.mat -applyxfm -out frontal_mask
> results in a frontal mask which is now at the back of the brain
> (picture attached), though it remains on the left.
>
> Note that the left_frontal_lobe mask was originally in the same
> space as the avg152T1 file provided with fsl..
> Overlay of the mask on the template was fine.
> So, I am now worried that the registration was wrong between the
> spgr and the avg152T1.
> How can I check?
>
> Thanks so much for your generosity with your time.
>
> -Dianne
>
> --
> Dianne Patterson, Ph.D.
> [log in to unmask]
> ERP Lab
> University of Arizona
> 621-3256 (Office)
>
> --
> Dianne Patterson, Ph.D.
> [log in to unmask]
> ERP Lab
> University of Arizona
> 621-3256 (Office)
> <Left_frontallobe_bad_transform.jpg>
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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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