The paper describing the algorithm used for EPI-to-structural registration in 3dAllineate has now been published:
ZS Saad, DR Glen, G Chen, MS Beauchamp, R Desai, and RW Cox.
A new method for improving functional-to-structural MRI alignment using local Pearson correlation. NeuroImage, 44: 839-848, 2009.
[
dx.doi.org]
For your reading pleasure, a copy can be found on our server at
[
afni.nimh.nih.gov]
[
afni.nimh.nih.gov]
Movie rights have been sold, and George Clooney will appear in the role of Ziad Saad.
Also, I recently made a minor addition to 3dAllineate to implement a new '-final' interpolation method: 'wsinc5' which is a 10x10x10 weighted (tapered) sinc interpolation scheme. This method is highly accurate and should preserve edge features and time series variances well, but is also several times slower than the next most accurate method in the software ('quintic', which uses a 6x6x6 interpolation stencil).
