Dear Mark,
Thank you so much for your answer! I have tried to
quickly sum up the procedure that you have described just
to be sure that I got it right. Furthermore, I have some
questions. Would you mind to take a quick look at both?
1. Use flirt to register the DTI to the individual T1.
2. Use flirt AND fnirt to register the individual T1 to
the MNI T1-template.
3. Take the resulting transformation matrices to register
the DTI (the one that has been registered to the
individual T1) to the MNI T1-template.
Where would you do the brain extraction? At the end, after
the DTI has been registered to the MNI T1-template?
When registering the DTI to the individual T1, would you
recommend to use the b0 as input volume?
Is it necessary to use masking, when registering the DTI
to the individual T1 with flirt? I thought that it
wouldn’t, since the DTI and the T1 have “the same” lesion?
Thanks again - your help is greatly appreciated!
Best,
Theodor
On Tue, 22 Nov 2011 09:49:53 +0000
Mark Jenkinson <[log in to unmask]> wrote:
> 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
>>
===================
Theodor Rüber
Remigiusplatz 1
53111 Bonn
Tel.: 0228/24005219
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