Thanks. I don't have a fieldmap, so I tried using various types of
masks as weighting matrices. Several ventral slices were masked out to
prevent any effects of signal loss in the anterior/ventral temporal
lobe.
Also tried a larger mask that removes roughly ventral half of
the brain (including orbitofrontal areas), and it still wants to push
the
epi down. (I also tried physically removing slices, just in case the
weighting
option didn't work as expected, but that did not help either). Another
mask was created by thresholding out low signal areas in the bottom half
(but keeping eveything in the top half). This mask removes some inferior
frontal and some temporal areas. It is a little better, but the problem
persists.
thanks,
Rutvik
On Sep 26, 2006, at 4:36 PM, Mark Jenkinson wrote:
> Hi,
>
> I've seen similar things before. The best solution is usually to
> apply
> unwarping and signal loss masking, as often the incorrect translation
> is an attempt to match up the inferior frontal area, which has little
> signal in the epi, with the background.
>
> Do you have a fieldmap?
> If so, I recommend using fugue for the registration - which is
> easiest through the Feat GUI. If not, then I suggest making a
> mask by hand which is zero in the areas that have signal loss
> and one everywhere else (including the background areas
> adjacent to parts of the brain that have good signal). Then
> try using this mask as a cost function weighting in flirt.
>
> Hopefully one of these will fix the problem.
> Let us know how you get on.
>
> All the best,
> Mark
>
>
> On 26 Sep 2006, at 20:15, Rutvik Desai wrote:
>
>> I am trying to register an epi to an anatomy using flirt to get
>> better alignment. The anatomy has
>> been skull-stripped. The anatomy is 256X256X134, with
>> 0.81x0.81x1.0 mm voxels. The epi is
>> 64x64x36, with 3.25x3.25x3.30 mm voxels. Seems that flirt always
>> wants to push the epi down (in
>> z direction, ventrally). I have tried various things, inlcluding
>> chopping off the bottom parts of
>> anatomy and/or the epi. This happens with a number of subjects.
>> Typically the epi is 2-3mm too
>> high, and is pushed down by 5-6 mm, making it too low. I have also
>> tried all cost functions, and
>> tried reducing the 'finesearch' value to 6 and 8 from 18. Any help
>> would be appriciated. I can send
>> an anat and an epi if necessary. Thanks!
>>
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