Thanks Mark!
On Fri, Feb 21, 2014 at 1:14 AM, Mark Jenkinson
<[log in to unmask]> wrote:
> Hi,
>
> You need to look carefully at the images and look at where the white matter / grey matter border is.
> This should allow you to distinguish between problems of stretching the outer CSF and problems of uncorrect distortions. It is likely that you will find uncorrected distortions in some areas of the image if you have not used fieldmaps, but other areas should hopefully be OK.
>
> All the best,
> Mark
>
>
> On 18 Feb 2014, at 18:13, "Xue, Feng" <[log in to unmask]> wrote:
>
>> Thanks Mark,
>>
>> Unfortunately, we didn't acquire fieldmap images. Hope it is because
>> of the outer CSF, but is there any way that I can make it for sure?
>>
>> Thanks.
>>
>> On Sun, Feb 16, 2014 at 2:54 PM, Mark Jenkinson
>> <[log in to unmask]> wrote:
>>> Hi,
>>>
>>> It looks like you might have some residual distortions left in the images.
>>> Have you used any form of fieldmap correction for the EPI distortions?
>>>
>>> Another possibility is that the outer CSF is stretched by the non-linear registration, but only in parts outside of the brain. If that is the case, and the grey matter / CSF boundary is correctly aligned, then you can ignore anything that happens to CSF outside of the brain.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>>
>>> On 14 Feb 2014, at 08:02, "Xue, Feng" <[log in to unmask]> wrote:
>>>
>>>> Dear experts,
>>>>
>>>> We encountered a registration problem(please see attached images).
>>>> There is a large mismatch between example func and standard. This
>>>> happens among several subjects while others are good. I checked images
>>>> from bet and it looks good(FYI, we used -B and -f 0.25 as parameters
>>>> for bet). So my questions are:
>>>> Is it acceptable?
>>>> If not, what should I do to improve it?
>>>>
>>>> Sorry, have to send in two emails, this is the first one.
>>>>
>>>> Thanks.
>>>> <example_func2standard.gif>
>>
>>
>>
>> --
>> Best Regards
>>
>> Xue, Feng Ph.D.
>>
>> Psychology Department
>> University of Southern California
>> Los Angeles CA, 90089
>> Mobile: +1 213-249-1040
>> ==============================================
>> National Key Laboratory of Cognitive Neuroscience and Learning
>> Beijing Normal University
>> Beijing, China. 100875
>> Mobile: +86 13810154455
>> web: http://psychbrain.bnu.edu.cn
--
Best Regards
Xue, Feng Ph.D.
Psychology Department
University of Southern California
Los Angeles CA, 90089
Mobile: +1 213-249-1040
==============================================
National Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China. 100875
Mobile: +86 13810154455
web: http://psychbrain.bnu.edu.cn
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