Dear Theodor,
You definitely need to use masking to get this to work.
We have had success previously in dealing with hemispherectomy
patients so I know it is possible. The trick is in getting the mask
right, so that it is zero in the missing hemisphere, but ones everywhere
else, including the background and the skull/scalp areas. If you do
this, and try various options for cost functions then you should be
able to get the registrations to work. Note that you are likely to be
best off trying to get the DTI-T1 registration to work first with FLIRT
only (trying various cost functions potentially and making sure that
the orientations start similarly - ideally use fslreorient2std on each
first). Then try to get that individual's T1 registered to the MNI
T1 template, initially with FLIRT and then with FNIRT. The latter
may be trickier and you may need to be very careful with the
mask and possibly change the control point spacing and/or the
regularisation parameters, but start with the standard config file
and a good mask and see how you get on.
All the best,
Mark
On 21 Nov 2011, at 17:07, Theodor R?ber wrote:
> Dear FSL-Experts,
>
> I have a bunch of DTI-datasets of patients who have undergone functional hemispherectomy. Since I want to run voxelwise analyses, I need to normalize these highly deformed brains.
>
> I have tried to normalise the FA-maps to the MNI-template using flirt/fnirt and masking out the lesions but the results were not really convincing. Do you have any advice on how the normalisation could be done best?
>
> Any input on this is highly appreciated.
> Thanks in advance!
>
> Best,
>
> Theodor
>
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