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Currently, there are three methods to align a functional session to a reference volume. These methods all assume you have a mrVista session initialized, with a set of T1-weighted Inplane anatomies that are co-registered to your functional data, as well as a high-quality reference anatomy. Look further down the page for alignment options where you don't have inplane anatomies.

This method uses mrRx ("mister prescribe") for applying affine transformations to a volume and aligning data within a session to a reference volume. rxAlign calls this tool in such a way that the vAnatomy is transformed, and compared to the inplane anatomies for the functional session. In addition to tools for manual alignment, it has implementations of some automatic alignment methods as well (computing a coarse alignment from image headers, using the SPM mutual information tool, and using the robust registration algorithm described by Nestares et al). rxAlign save the results as a 4x4 transform directly in the mrSESSION.alignment field.

This function uses a combination of the anatomical headers (for both the vAnatomy and inplane anatomies) and the SPM mutual information code to compute an automated alignment and provide feedback on how well the alignment worked. The method works particularly well on aligning whole-brain inplanes. We also use it for surface-coil images, but in that case it can fail. Under such conditions, it is best to use rxAlign. The core algorithm for mrAlignMI can also be called from within rxAlign. [mrAlignMI]], save the results as a 4x4 affine transforms directly in the mrSESSION.alignment field.


[edit] Whole-brain to whole-brain alignment

Another alignment option exists for the case where you have functionals and a whole-brain T1 anatomy from a scanning session, but no inplane anatomies. This is called whole-brain alignment, because it relies on the high accuracy of current co-registration methods for aligning whole-brain anatomies to one another. This whole-brain to whole-brain alignment maps between the "volume anatomy", which is the high-quality reference anatomy described in the Anatomical_Methods section, and the whole-brain anatomy collected during the functional session. This alignment is combined with header information to map between the within-session whole-brain anatomy and the functionals to produce a final alignment.

Development of this code is underway, and expected to be completed by mid October 2009. See the Whole-brain Alignment page for details.

[edit] SPGR SEIR Alignment

The SPGR SEIR Alignment page explains how to align SPGR and SEIR images to an anatomical T1 image, then, to each other.

[edit] References

[edit] Mutual Information Alignment

(These citations are from the documentation for spm_coreg; the core of that function was written by John Ashburner; many thanks!)

  • Template:Note Collignon, Maes, Delaere, Vandermeulen, Suetens & Marchal (1995). "Automated multi-modality image registration based on information theory". In Bizais, Barillot & Di Paola, editors, Proc. Information Processing in Medical Imaging, pages 263--274, Dordrecht, The Netherlands, 1995. Kluwer Academic Publishers. [Mutual Information]
  • Template:Note Wells III, Viola, Atsumi, Nakajima & Kikinis (1996). "Multi-modal volume registration by maximisation of mutual information". Medical Image Analysis, 1(1):35-51, 1996. [Mutual Information]
  • Template:Note F Maes, A Collignon, D Vandermeulen, G Marchal & P Suetens (1997). "Multimodality image registration by maximisation of mutual information". IEEE Transactions on Medical Imaging 16(2):187-198 [Entropy Correlation Coefficient]
  • Template:Note Studholme, Hill & Hawkes (1998). "A normalized entropy measure of 3-D medical image alignment". in Proc. Medical Imaging 1998, vol. 3338, San Diego, CA, pp. 132-143. [Normalized Mutual Information]
  • Template:Note Press, Teukolsky, Vetterling & Flannery (1992). "Numerical Recipes in C (Second Edition)". Published by Cambridge. [Optimisation]

[edit] Robust Multi-Image Registration

  • Template:Note Nestares O, Heeger DJ, 2000 Robust multiresolution alignment of MRI brain volumes. Magn Reson Med. 43(5):705-15.
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