Hi,
If your activations are in the empty space on the functional images then this can have nothing to do with registration, as the registration will only determine how this appears in the structural or MNI spaces (and in the latter there would be no wide sulci).
As a separate point, the registrations you show look fairly reasonable, although there are still residual distortions that are not corrected for, but you must have a fieldmap (or blip-up-blip-down equivalent) in order to fix this.
In terms of the location of activations in the functional space, if you are finding things in the wrong location then it might point to artifacts or bad motion correction. If you are using multiband data then are you using a separate motion correction target image (e.g., the single band reference image)? This might be a cause of some of the problems.
All the best,
Mark
> On 3 Nov 2017, at 12:04, SUBSCRIBE FSL Yuqi Liu <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> We are analyzing data from stroke patients who are mostly elderly, so their brains had lesions and wide sulci. When looking at their data for hand movements, we found activation centered on empty space between precentral and postcentral gyri, but not on any gyri. I am wondering if it is because our patients have wide sulci, so something went wrong with registration (for example, FSL is treating the empty as grey matter). For registration, we did BBR and 6 DOF from functional to structural space (we are not aligning to MNI space), although we don't have a field map scan.
>
> I am attaching registration summary figures and results in this link:
> https://www.dropbox.com/sh/vtio0ajelhwrymb/AADLfI92hyc2h9EaRKYr_8bLa?dl=0
>
> Another thing I should mention is that, we are using CMRR multiband sequence and 64-channel head coil. This could make the contrast of structural image tricky, as we always have to lower the fractional intensity for BET. Maybe it potentially causes registration problem (e.g. poor contrast between white matter and grey matter)?
>
> So my question is, is it a registration problem or something else? If it is a registration problem, what can we do to fix it? And if is other problems, what can we do or try to fix it?
>
> Thank you very much!
> Yuqi
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