Hi,
I am not sure if this still is the recommended solution, but one way to
cope with it is not adjusting the sizes of the search in mcflirt, but
instead rescale the voxel dimensions of the data, so that the search
steps of mcflirt make more sense. So in your case, you might want to
multiply the voxel size by 8.
I myself prefer using a script that applies flirt volume-wise. This way
I have a better control of the co-registration.
Good luck,
wolf
On 12/27/2012 07:38 PM, Ben Jarrett wrote:
> Hello All,
>
> I have some small animal brain volumes I'd like to apply mcflirt to for motion correction, but it does a terrible job as the voxel size is too small. Looking at the mcflirt function it appears to start with a course 8mm search followed by a 4mm refined search; and I suspect this search is the problem as 4mm is still far larger than any dimension of my voxel size.
>
> Is there any way to narrow the search range? Say start with 1mm and refine to 0.5mm?
>
> Thanks
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