UCLA Brain Mapping Center

Automated Image Registration (AIR)

Primary References One or more of the following references should be cited in any paper based on data registered using the AIR package or programs utilizing the AIR library.

• Woods RP, Cherry SR, Mazziotta JC. Rapid automated algorithm for aligning and reslicing PET images. Journal of Computer Assisted Tomography 1992;16:620-633.
  The original AIR manuscript validating the intramodality method implemented in AIR 1.0.
• Woods RP, Mazziotta JC, Cherry SR. MRI-PET registration with automated algorithm. Journal of Computer Assisted Tomography 1993;17:536-546.
  The method used for intermodality registration as implemented in AIR 1.0.
• Woods RP, Grafton ST, Holmes CJ, Cherry SR, Mazziotta JC. Automated image registration: I. General methods and intrasubject, intramodality validation. Journal of Computer Assisted Tomography 1998;22:139-152.
  Description of AIR 3.0 and validation for intrasubject, intramodality registration of MRI data and intrasubject, intramodality registration of PET data.
• Woods RP, Grafton ST, Watson JDG, Sicotte NL, Mazziotta JC. Automated image registration: II. Intersubject validation of linear and nonlinear models. Journal of Computer Assisted Tomography 1998;22:153-165.
  Validation of AIR 3.0 for intersubject registration.

Secondary References The following references provide additional validation of AIR.

• Strother SC, Anderson JR, Xu XL, Liow JS, Bonar DC, Rottenberg, DA. Quantitative comparisons of image registration techniques based on high-resolution MRI of the brain. Journal of Computer Assisted Tomography 1994;18:954-62.
  A comparative study using simulations that included AIR 1.0.
• Jiang AP, Kennedy DN, Baker JR, Weisskoff R, Tootell RBH, Woods RP, Benson RR, Kwong KK, Brady TJ, Rosen BR, Belliveau JW. Motion detection and correction in functional MR imaging. Human Brain Mapping 1995;3:224-235.
  Validation of AIR 1.0 in the context of fMRI.
• Black KJ, Videen TO, Perlmutter JS. A metric for testing the accuracy of cross-modality image registration: Validation and application.Journal of Computer Assisted Tomography 1996;20:855-861.
  AIR MRI-PET registration validation in monkeys.
• West J, Fitzpatrick JM, Wang MY, Dawant BM, Maurer CR, Kessler RM, Maciunas RJ, Barillot C, Lemoine D. Collignon A, Maes F, Suetens P, Vandermeulen D, van den Elsen P, Napel S, Sumanaweera TS, Harkness B, Hemler PF, Hill DLG, Hawkes DJ, Studholme C, Maintz JBA, Viergever MA, Malandain G, Pennec X, Noz ME, Maguire GQ, Pollack M, Pelizzari CA, Robb RA, Hanson D, Woods RP. Comparison and evaluation of retrospective intermodality brain image registration techniques. Journal of Computer Assisted Tomography 1997;21:554-566.
  AIR 1.0's MRI-PET registration technique in a comparative blinded study.
• Imran MB, Kawashima R, Sat K, Kinomura S, Ito H, Koyama M, Goto R, Ono S, Yoshioka S, Fukuda H. Mean regional cerebral blood flow images of normal subjects using technetium-99m-HMPAO by automated image registration. Journal of Nuclear Medicine 1998;39:203-207.
  Use of AIR for intersubject registration of HMPAO-SPECT images.

BrainSuite

The BrainSuite software collection represents the scholarly work of several investigators. If you use BrainSuite in your research, you should cite the appropriate articles. We have compiled the list below as a guide to which article describe which components of the software.

 

BrainSuite (and below articles as appropriate)

• Shattuck DW and Leahy RM (2002) BrainSuite: An Automated Cortical Surface Identification Tool Medical Image Analysis 8(2):129-142.

TCA

• Shattuck DW and Leahy RM (2001) Graph Based Analysis and Correction of Cortical Volume Topology IEEE Transactions on Medical Imaging 20(11):1167-1177.

BSE,BFC,PVC

• Shattuck DW, Sandor-Leahy SR, Schaper KA, Rottenberg DA, and Leahy RM (2001) Magnetic Resonance Image Tissue Classification Using a Partial Volume Model NeuroImage 13(5):856-876.

BSE

• Sandor S and Leahy R (1997) Surface-based labeling of cortical anatomy using a deformable database IEEE Transactions on Medical Imaging 16(1):41-54.

Cerebrum Extraction Tool

• Woods RP, Grafton ST, Holmes CJ, Cherry SR, Mazziotta JC. (1998) Automated image registration: I. General methods and intrasubject, intramodality validation. Journal of Computer Assisted Tomography 22:139-152.
• Woods RP, Grafton ST, Watson JDG, Sicotte NL, Mazziotta JC. (1998) Automated image registration: II. Intersubject validation of linear and nonlinear models. Journal of Computer Assisted Tomography 22:153-165.

MultiTracer

• Woods RP. (2003) Multitracer: a Java-based tool for anatomic delineation of grayscale volumetric images. NeuroImage 19(4):1829-34.

ShapeTools

• Joshi SH, Cabeen RP, Sun B, Joshi AA, Gutman B, Zamanyan A, Chakrapani S, Dinov I, Woods RP, Toga AW. (2010) Cortical sulcal atlas construction using a diffeomorphic mapping approach. Med Image Comput Comput Assist Interv. 13(Pt 1):357-66.
• Joshi SH, Cabeen RP, Joshi AA, Woods RP, Narr KL, Toga AW. (2010) Diffeomorphic Sulcal Shape Analysis for Cortical Surface Registration. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 13-18 June:475-482.
• Joshi SH, Cabeen RP, Joshi AA, Sun B, Dinov I, Narr KL, Toga AW, Woods RP. (2012) Diffeomorphic sulcal shape analysis on the cortex. IEEE Trans Med Imaging. 31(6):1195-212.

SHIVA

• MacKenzie-Graham A, Lee EF, Dinov ID, Bota M, Shattuck DW, Ruffins S, Yuan H, Konstantinidis F, Pitiot A, Ding Y, Hu G, Jacobs RE, Toga AW. (2004) A multimodal, multidimensional atlas of the C57BL/6J mouse brain. J Anat. 204(2):93-102.