That actually looks fine to me too. When FEAT creates a mask of the brain, it extends the mask out a bit to make sure that it does not cut off any brain. Every voxel in the mask will get a zstat. If your raise the threshold a bit, the stuff outside of the brain will probably drop away.
doug
On 8/31/11 6:10 PM, noam Schneck wrote:
Sure thing, attached to this email are two sets of images. One includes the tkregister2 outputs in which the movable is the example func. Based on the surface the registration looks good. The other image is the zstat from that same run (in EPI space) overlayed onto the anatomical using the same registration matrix that I used in the tkregister2 output (this is seen in the tkmedit output). What you can see is that the zstat activation map extends outside of the brain and skull, despite using a registration matrix that produced a good registration when just looking at the grey white matter boundary. if it would be helpful I can also send you images of what the example_func overlayed onto the anatomical in tkmedit looks like. It basically shows that the examplefunc extends outside the borders of the skull. I would have included it but it exceeds the email KB limit.
Thanks so much for taking the time, noam
I see, thank you so much for your time.
Noam
On Wed, Aug 31, 2011 at 10:58 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
That actually looks fine to me too. When FEAT creates a mask of the brain, it extends the mask out a bit to make sure that it does not cut off any brain. Every voxel in the mask will get a zstat. If your raise the threshold a bit, the stuff outside of the brain will probably drop away.
doug
On 8/31/11 6:10 PM, noam Schneck wrote:
Sure thing, attached to this email are two sets of images. One includes the tkregister2 outputs in which the movable is the example func. Based on the surface the registration looks good. The other image is the zstat from that same run (in EPI space) overlayed onto the anatomical using the same registration matrix that I used in the tkregister2 output (this is seen in the tkmedit output). What you can see is that the zstat activation map extends outside of the brain and skull, despite using a registration matrix that produced a good registration when just looking at the grey white matter boundary. if it would be helpful I can also send you images of what the example_func overlayed onto the anatomical in tkmedit looks like. It basically shows that the examplefunc extends outside the borders of the skull. I would have included it but it exceeds the email KB limit.
Thanks so much for taking the time, noam
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