Hi wolf,
Without seeing the data it is difficult to be precise, but in general,
surface coil data is difficult to register because of the large bias
field effects in it. The best remedy for this (if you can't remove
the bias field by some form of calibration) is to weight the surface
coil image such that regions of high signal have a near unity
weight and regions where the signal is low receive near zero weight.
You'll probably need to define this by hand, and to start with a simple
binary mask, drawn in fslview might suffice.
As for scaling and mcflirt - if you have a whole brain volume then
mcflirt should work well regardless of the input resolution. However,
if you are dealing with a small FOV, then it may have problems still
(as it works at 8mm and 4mm resolutions) and "rescaling" the voxel
dimensions by an appropriate factor may work better. Alternatively,
you can script flirt up to do the same job if that's easier.
All the best,
Mark
wolf zinke wrote:
> Hi,
>
> I was happy to read that rescaling is not an issue anymore for flirt.
> Is it the same for mcflirt, or does this function still require data
> with the right scales.
>
> I was trying now to apply flirt to my data and wanted to coregister a
> coronal set of slices acquired with a surface coil to a full brain
> scan, both T1 weighted sequences. The results are not satisfying me. I
> was playing around with the cost functions and the DOF, but got no
> acceptable results. Are there any suggestions, how to achieve a good
> coregistration.
>
> thanks,
>
> wolf
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