If you've already run the Realignment module and have r* images, those
are already aligned to the mean EPI, so if you Coregister using the mean
EPI as the "Reference Image" and SPGR as the "Source Image", there is no
need to select "Other Images" -- the SPGR will be coregistered into the
space of the mean EPI, which is the same space that the r* EPI images
are already in from the realignment step.
functional , On Sat, 2010-12-18 at 16:47 -0500, MCLAREN, Donald wrote:
> Things that would be better:
> (1) Use SPM8
> (2) Switch the reference and source images and then you don't need to
> select any images
> The T1 will then be in line with the EPI.
> Best Regards, Donald McLaren
> D.G. McLaren, Ph.D.
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Research Fellow, Department of Neurology, Massachusetts General
> Hospital and Harvard Medical School
> Office: (773) 406-2464
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> On Sat, Dec 18, 2010 at 4:37 PM, John Gelburg <[log in to unmask]>
> Currently I am doing the SPGR-EPI co-registration in the
> following way and I see that the images do not exactly match.
> 1. Coreg: Estimate option
> 2a. Reference Image: mean image from realignment step
> 2b. Source Image: SPGR image
> 2c. Other images: all the EPI images
> In the subsequent steps I segment the co-registred SPGR image
> and then use the *_sn.mat for normalization.
> What can I do better? It's desirable to be able to run the
> whole process automatically.