On Wed, Oct 15, 2008 at 10:10:57AM +0100, Mark Jenkinson wrote:
> Hi Michael,
>
> I would try scripting flirt and see how that performs. In general
> flirt will be more robust to things like limited FOV so hopefully that
> will help. Use the -nosearch option with this kind of data though, as
> that will help it.
Thanks for your suggestions.
I took the 4d image apart and ran flirt on each 3d image individually --
it is not yet perfect, but when using -2D, a lot more stable than
before. It gets even better when using the deweighting approach
suggested by Andreas (using an mask covering the medial parts of the
brain, excluding two edge slices on top and bottom).
The thing it still cannot deal with are slight rotations around x-axis
(ie. nods) -- quite plausible with -2D. However, doing -dof 6 it does not
yield a stable alignment across the timeseries, regardless of
deweighting enabled or not.
Is there anything I could try to handle the nods?
I am also interested in generating parameter output as mcflirt's -plots
option would do -- is there a way to do that on the command line?
Thanks again,
Michael
> On 15 Oct 2008, at 10:00, Michael Hanke wrote:
>
>> Hi,
>>
>> I have a dataset with 12 ZOOM-EPI slices (FOV 13cm), parallel to the
>> calcarine sulcus, covering approx. 2/3 of the brain in
>> ant.-post-direction.
>>
>> There is a slight drift in the data along the y axis, which I want to
>> remove with mcflirt. However, mcflirt doesn't really like the data,
>> ie.
>> after correction, there are all kinds of additional (visible) motion
>> in
>> the dataset. I tried -2d, -gdt, -edge, -fov options, but could not
>> achieve significant improvements. Especially the slow drift still
>> remains in the data.
>>
>> I guess the problem is that the FOV barely covers the brain from left
>> to
>> right and only has the posterior parts. (screenshot is attached)
>>
>> Does anyone have experience with this kind of data and maybe
>> suggestions
>> what to try next? The amount of motion is more than I could tolerate
>> for the intended analysis, so I cannot simply ignore it.
>>
>> Thanks in advance,
>>
>> Michael
>>
>> --
>> GPG key: 1024D/3144BE0F Michael Hanke
>> http://apsy.gse.uni-magdeburg.de/hanke
>> ICQ: 48230050
>> <zoom-epi.png>
--
GPG key: 1024D/3144BE0F Michael Hanke
http://apsy.gse.uni-magdeburg.de/hanke
ICQ: 48230050
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