Hi,
Thank you for replying.
The problem looks the same as the image which Barbara showed. This subjects moved during data acquisition. I also tried to use mcflirt to do registration and eddy current correction, but some images were blur. Is there any solution or I have to discard this image?
Thanks again!
Best,
Xiaozhen
Xiaozhen Li
Department of Neurobiology, Care Sciences and Society
Division of Clinical Geriatrics
Karolinska University Hospital
Novum, Plan 5, Huddinge
141 86 Stockholm
Sweden
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Kreilkamp Barbara Anne Katharina [[log in to unmask]]
Sent: Thursday, September 05, 2013 10:34 AM
To: [log in to unmask]
Subject: Re: [FSL] eddy current correction
Hi Xiaozhen,
May I put in my two cents? I once had the same problem...
This could be a 'reslicing' problem. I had encountered it on my DTI data for one participant. The problem was that this participant had moved so much, that the last two slices were 'cut' after eddy correction.
If the participant moves (rotates) during an acquisition of the slices the slices are no longer in correct orientation, so with eddy_correct they are being 'resliced' to go back to the original orientation.
Now, if this occurred in one of the first/last slices that you are interested in there is no information anymore to build up the last slice again.
When doing the acquisition you would want to make sure to include one slice before and after the ones you are interested in.
Does it look something like the axial slice I attached as a screenshot?
Best,
Barbara
[cid:232b4ff8-6efa-4746-9dd0-d42f1bd01b05@user.ki.se]
Am 05.09.2013 um 08:38 schrieb Mark Jenkinson:
> Hi,
>
> It is difficult to help without more information.
> My guess would be that your registration has failed, but I would need to know more in order to help.
>
> All the best,
> Mark
>
>
> On 4 Sep 2013, at 22:08, Xiaozhen Li <[log in to unmask]> wrote:
>
>> Hi, I run eddy_correct for DTI data. The part of the brain was cut. I have never met something like this. What is wrong with it? How could I fix that?
>>
>> Thanks a lot!
>>
>> Best,
>> Xiaozhen
>>
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