Hi,
>elderly often have a high signal from the fat in the marrow of the skull
>bone
Yes, because the blood-building bone marrow gets replaced by fat in the
elderly.
>so first using FLIRT for registration of the functional to structural
>images (Normal Search, 12 DOF)
Julia - you should use 6 (no more than 7) DOFs here because this is an
within-subject registration problem.
I assume that this wonąt solve the issue, though.
Cheers,
Andreas
Am 30.03.16, 17:03 schrieb "FSL - FMRIB's Software Library on behalf of
Jesper Andersson" unter <[log in to unmask] on behalf of
[log in to unmask]>:
>Dear Julia,
>
>elderly subjects can sometimes be a bit tricky. On the one hand the large
>ventricles means that one needs to do non-lin reg. On the other hand I
>have observed that elderly often have a high signal from the fat in the
>marrow of the skull bone. Since that signal is not present in the MNI
>template one sometimes see cases where that marrow signal at the crown of
>the head gets registered to the top part of the brain in the MNI. You can
>then get the effect you see.
>
>One can sometimes solve the problem by experimenting a little with how
>the masking is applied.
>
>Jesper
>
>On 30 Mar 2016, at 15:26, Julia Schumacher <[log in to unmask]>
>wrote:
>
>> Dear FSL experts,
>>
>> I am trying to do registration on data from elderly dementia patients
>>with quite large amounts of atrophy and enlarged ventricles.
>> I am performing a two-step registration procedure using the MELODIC
>>GUI, so first using FLIRT for registration of the functional to
>>structural images (Normal Search, 12 DOF) and then using FNIRT for the
>>nonlinear registration of structural (and functional) images to the
>>MNI152 template (Normal Search, 12 DOF, 10 mm warp resolution).
>> The first step works fine.
>> However, the nonlinear registration of the structural to standard image
>>results in bad registrations for some of the subjects where the upper
>>part of the brain seems to get pulled in
>>(https://www.dropbox.com/s/qd6krdkfvkcn2fa/highres2standard_nonlin.png?dl
>>=0).
>> We thought that the problem might be caused by FNIRT trying to align
>>the enlarged ventricles with the much smaller ventricles of the template
>>and thereby pulling the rest of the brain in.
>> So, I also tried using linear registration for both steps, which
>>results in nicely registered brain boundaries, but then obviously the
>>ventricles and subcortical structures are registered poorly (see
>>https://www.dropbox.com/s/r1dsputl0ksllw4/highres2standard_lin.png?dl=0).
>>
>> Has anyone experienced similar problems with brains that show atrophy
>>and large ventricles?
>> Is there any solution to this? Specifically, is there any way to adjust
>>FNIRT parameters to maybe prevent this problem or to find a tradeoff
>>between good registration of the ventricles and good registration of the
>>cortex?
>>
>> I would be very grateful for any help!!
>> I am also happy to provide more data if that helps.
>> Kind regards,
>> Julia
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