Hi Mark,
On Thu, Oct 16, 2008 at 07:37:17AM +0100, Mark Jenkinson wrote:
> Hi Michael,
>
> Generating mcflirt-style parameter outputs is relatively
> easy. Just run avscale with the --allparams option and
> grep out the required lines for Rotation Angles and
> Translations.
Ah! Thanks for the hint.
> As for getting a good estimate of through plane
> effects from such a small ROI - I'm just not sure as
> it will depend on how good the data is and how
> big the rotations are. Can you upload the data for
> me to have a look at?
Done so -- session id is 362942.
This is a single run, no preprocessing whatsoever.
Thanks for thanking a look at it!
Best,
Michael
> On 15 Oct 2008, at 13:00, Michael Hanke wrote:
>
>> 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
>>
--
GPG key: 1024D/3144BE0F Michael Hanke
http://apsy.gse.uni-magdeburg.de/hanke
ICQ: 48230050
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