Dear Hongyu,
If it is not a registration-related problem then you can simply
ignore it. Activations outside the brain rarely survive group
analysis and can simply be ignored if they do as it is known
that artefacts in fMRI (e.g. ghosting) can cause this.
All the best,
Mark
On 5 Mar 2010, at 19:56, 杨宏宇 wrote:
> Hi Mark,
>
> I checked that, and found the activated areas were beyond the brain
> before registration, which means this is not a registration problem.
> O.K, I am relaxed now. And, if it is not, then what problem is this?
> Is it serious? How can we solve and removed it?
>
> Many thanks,
> Hongyu
>
> 2010/3/5 Mark Jenkinson <[log in to unmask]>:
>> Dear Hongyu,
>>
>> I'm uncertain as to whether you have a registration problem
>> or whether you simply have a large brain mask and some
>> activations in the mask which are technically outside the brain.
>> This is not uncommon due to ghosting and other acquisition-related
>> issues, and is no real problem. If you look at your first level
>> results,
>> which are shown on the original functional images, then you can
>> figure out whether you have activations outside of the brain like
>> this or not. If you do, then your problem has nothing to do with
>> registration, as the first level results do everything on the
>> original
>> functional images and do not use any registration results. However,
>> if you do not see any activations outside of the brain in the first
>> level results but then see them at higher levels then this is
>> likely to
>> be a registration-related issue.
>>
>> Can you let us know which it is?
>>
>> All the best,
>> Mark
>>
>> On 4 Mar 2010, at 20:22, Hongyu Yang wrote:
>>
>>> Hi Mark,
>>>
>>> We checked all the registration page results, based on our limited
>>> experience, they were OK. We even compared the results with the
>>> previous
>>> results we got before, in which the activated areas of post-stats
>>> were
>>> matched with the background brain image, still could not find some
>>> obvious
>>> differences between the two. I tried to use some introduction from
>>> FLIRT,
>>> which said If we want to register fMRI data with only a few slices,
>>> following the instructions of this link:
>>>
>>> http://www.fmrib.ox.ac.uk/fsl/flirt/ztrans.html
>>>
>>> However, I still got similar results, activated areas beyond the
>>> background
>>> brain image. One of my colleague said he don't think it's a
>>> registration
>>> problem. He think we have noisy voxels outside brain that happen to
>>> follow
>>> the model, and then don't get masked out because the brain mask is a
>>> little
>>> bigger than brain. I can not agree with his points, however, I do
>>> not know
>>> what problem caused this consequence. Can I send some results to
>>> you, and
>>> can you help us to come out from the dilemma, which bothers us for
>>> a very
>>> long time.
>>>
>>>
>>>
>>>
>>
>>
>
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