Thanks:)
On Thu, Sep 17, 2009 at 11:24 PM, Mark Jenkinson <[log in to unmask]> wrote:
> 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
>> ==============================================
>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University
>> telnet://bbs.mdjs.org
>> http://bbs.mdjs.org
>>
>
--
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
==============================================
Welcome to MuDuo JinSheng BBS @ Beijing Normal University
telnet://bbs.mdjs.org
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