Hi,
Some very atrophied old brains are indeed challenging, and the
standard defaults may not work. However, we are able to get
registrations to work on most brains. If you have a specific
example that you cannot get to work then feel free to upload it
and we will see if we can find the right settings to get it to work.
All the best,
Mark
On 17 Sep 2009, at 16:21, Xue, Feng wrote:
> It seems that Flirt/Fnirt have the problem too. I've done registration
> on some old brains, one of them was bad:(
>
> On Thu, Sep 17, 2009 at 11:06 PM, Eldreth, Dana A.
> <[log in to unmask]> wrote:
>> Hi Mark,
>>
>> Thanks! I will see how this technique works out.
>>
>> Best Regards,
>> Dana
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
>> Of Mark Jenkinson [[log in to unmask]]
>> Sent: Monday, September 14, 2009 3:33 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] FIRST in Older Brains
>>
>> Hi,
>>
>> We've been experimenting with a few things over the summer
>> but do not have a single solution that works in all cases. It
>> depends on how severe the atrophy is, but it can be quite
>> beneficial to do a non-linear registration to the MNI152
>> and then apply FIRST to the output. This doesn't always
>> do a good job and in severe atrophy it isn't great, but it
>> can really help in a lot of cases.
>>
>> You will then need to apply the mask to the original image
>> using an inverse warp. To make sure that this doesn't take
>> too long, make sure that you crop your original image to
>> exclude as much non-brain as possible. Then run the
>> fnirt and the invwarp should be relatively efficient. If you
>> original image is very high resolution though, it may be
>> helpful to make a new reference image with the same FOV
>> but a larger voxel size (1mm or even 2mm) to act in place
>> of the original image, just for the purposes of invwarp.
>>
>> Hope this helps.
>> If you still have problems please let us know, and we'll keep
>> everyone posted on progress with FIRST and atrophied
>> brains.
>>
>> All the best,
>> Mark
>>
>>
>>
>> On 9 Sep 2009, at 00:57, Dana Eldreth wrote:
>>
>>> Dear FSL creators,
>>>
>>> I am running FIRST on some older brains that are very
>>> heterogeneous. For
>>> most, FIRST does an excellent job, but for some it is substantially
>>> off because
>>> of atrophy. Earlier in the summer there was talk of a modification
>>> to FIRST for
>>> older brains. I wanted to follow-up to see when that program may be
>>> available.
>>>
>>> I was wondering if there is a protocol recommendation for what
>>> should be
>>> done for subjects whose subcortical structures cannot be estimated
>>> well using
>>> FIRST. How should this be reported if some subjects need to be
>>> excluded?
>>>
>>> Eagerly waiting FIRST for older brains!
>>>
>>> Thanks!
>>> Dana
>>>
>>
>
>
>
> --
> Best Regards
>
>
> National Key Laboratory of Cognitive Neuroscience and Learning
> Beijing Normal University
> Beijing, China. 100875
> Tel: +86-13810154455
> web: http://psychbrain.bnu.edu.cn
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