Some Links

Jason's Home Page

Welcome to the homepage of this humble former PhD student here at the Brain Imaging Centre of the Montreal Neurological Institute. I'm currently a post-doctoral fellow at the Hospital for Sick Children and the Toronto Centre for Phenogenomics, where I'm focused on studying brain plasticity using MRI in mice.

My main PhD thesis work was related to measuring the thickness of the cerebral cortex in a fully automated fashion. This was applied to developing and aging populations as well as Alzheimer's Disease, but has many uses beyond that as well. Without further ado, here's a link to my PhD thesis.


If you've come to this site looking for software I've written, here are some useful links:
RMINC interfaces MINC volumes with the R statistical environment. The code is freely available.
build-model is a pipeline designed to create a consensus average from a set of 3D scans; most commonly used for mouse brains. Write if you'd like to use this code.
mni.cortical.statistics is a set of R functions to analyse cortical thickness maps (or any data represented on the cortex). The code is freely available.
brain-view is GUI application to view bits of geometry (such as models of the brain) along with data associated with each vertex (such as cortical thickness maps). The code is freely available.


  1. Watkins KE, Paus T, Lerch JP, Zijdenbos A, Collins DL, Neelin P, Taylor J, Worsley KJ, Evans AC. Structural asymmetries in the human brain: a voxel-based statistical analysis of 142 MRI scans. Cereb Cortex. 2001 Sep;11(9):868-77. [pdf]

  2. Worsley KJ, Taylor JE, Tomaiuolo F, Lerch J. Unified univariate and multivariate random field theory. NeuroImage. 2004;23 Suppl 1:S189-95. [pdf]

  3. Taki Y, Goto R, Evans A, Zijdenbos A, Neelin P, Lerch J, Sato K, Ono S, Kinomura S, Nakagawa M, Sugiura M, Watanabe J, Kawashima R, Fukuda H. Voxel-based morphometry of human brain with age and cerebrovascular risk factors. Neurobiol Aging. 2004 Apr;25(4):455-63. [pdf]

  4. Bernasconi N, Duchesne S, Janke A, Lerch J, Collins DL, Bernasconi A. Whole-brain voxel-based statistical analysis of gray matter and white matter in temporal lobe epilepsy. NeuroImage. 2004 Oct;23(2):717-23. [pdf]

  5. Lerch JP, Evans AC. Cortical thickness analysis examined through power analysis and a population simulation. NeuroImage. 2005 Jan 1;24(1):163-73. [pdf]

  6. Nagano-Saito A, Washimi Y, Arahata Y, Kachi T, Lerch JP, Evans AC, Dagher A, Ito K. Cerebral atrophy and its relation to cognitive impairment in Parkinson disease. Neurology. 2005 Jan 25;64(2):224-9. [pdf]

  7. Tomaiuolo F, Worsley KJ, Lerch J, Di Paola M, Carlesimo GA, Bonanni R, Caltagirone C, Paus T. Changes in white matter in long-term survivors of severe non-missile traumatic brain injury: a computational analysis of magnetic resonance images. J Neurotrauma. 2005 Jan;22(1):76-82.

  8. Bobb AJ, Addington AM, Sidransky E, Gornick MC, Lerch JP, Greenstein DK, Clasen LS, Sharp WS, Inoff-Germain G, Wavrant-De Vrieze F, Arcos-Burgos M, Straub RE, Hardy JA, Castellanos FX, Rapoport JL. Support for association between ADHD and two candidate genes: NET1 and DRD1. Am J Med Genet B Neuropsychiatr Genet. 2005 Apr 5;134(1):67-72. [pdf]

  9. Worsley KJ, Chen JI, Lerch J, Evans AC. Comparing functional connectivity via thresholding correlations and singular value decomposition. Philos Trans R Soc Lond B Biol Sci. 2005 May 29;360(1457):913-20. [pdf]

  10. Lerch JP, Pruessner JC, Zijdenbos A, Hampel H, Teipel SJ, Evans AC. Focal decline of cortical thickness in Alzheimer's disease identified by computational neuroanatomy. Cereb Cortex. 2005 Jul;15(7):995-1001. [pdf]

  11. Kim JS, Singh V, Lee JK, Lerch J, Ad-Dab'bagh Y, MacDonald D, Lee JM, Kim SI, Evans AC. Automated 3-D extraction and evaluation of the inner and outer cortical surfaces using a laplacian map and partial volume effect classification. NeuroImage. 2005 Aug 1;27(1):210-21. [pdf]

  12. Zijdenbos AP, Lerch JP, Bedell BJ, Evans AC. Brain imaging in drug R&D. Biomarkers. 2005 Nov;10 Suppl 1:S58-68. [pdf]

  13. Shaw P, Greenstein D, Lerch J, Clasen L, Lenroot R, Gogtay N, Evans A, Rapoport J, Giedd J. Intellectual ability and cortical development in children and adolescents. Nature. 2006 Mar 30;440(7084):676-9. [pdf]

  14. Dorsaint-Pierre R, Penhune VB, Watkins KE, Neelin P, Lerch JP, Bouffard M, Zatorre RJ. Asymmetries of the planum temporale and Heschl's gyrus: Relationship to language lateralization. Brain. 2006 May;129(Pt 5):1164-76. [pdf]

  15. Shaw P, Lerch J, Greenstein D, Sharp W, Clasen L, Evans A, Giedd J, Castellanos FX, Rapoport J. Longitudinal mapping of cortical thickness and clinical outcome in children and adolescents with attention-deficit/hyperactivity disorder. Arch Gen Psychiatry. 2006 May;63(5):540-9. [pdf]

  16. Lerch JP, Worsley K, Shaw WP, Greenstein DK, Lenroot RK, Giedd J, Evans AC. Mapping anatomical correlations across cerebral cortex (MACACC) using cortical thickness from MRI. NeuroImage. 2006 Jul 1;31(3):993-1003. [pdf]

  17. Hyde KL, Zatorre RJ, Griffiths TD, Lerch JP, Peretz I. Morphometry of the amusic brain: A two-site study. Brain. 2006 Oct;129(Pt 10):2562-70. [pdf]

  18. Greenstein D, Lerch J, Shaw P, Clasen L, Giedd J, Gochman P, Rapoport J, Gogtay N. Childhood onset schizophrenia: cortical brain abnormalities as young adults. J Child Psychol Psychiatry. 2006 Nov;47(10):1003-12. [pdf]

  19. Singh V, Chertkow H, Lerch JP, Evans AC, Dorr AE, Kabani NJ. Spatial patterns of cortical thinning in mild cognitive impairment and Alzheimer's disease. Brain. 2006 Nov;129(Pt 11):2885-93. [pdf]

  20. Giedd JN, Clasen LS, Wallace GL, Lenroot RK, Lerch JP, Wells EM, Blumenthal JD, Nelson JE, Tossell JW, Stayer C, Evans AC, Samango-Sprouse CA. XXY (Klinefelter syndrome): a pediatric quantitative brain magnetic resonance imaging case-control study. Pediatrics. 2007 Jan;119(1):e232-40. [pdf]

  21. Charil A, Dagher A, Lerch JP, Zijdenbos AP, Worsley KJ, Evans AC. Focal cortical atrophy in Multiple Sclerosis: Relation to lesion load and disability. NeuroImage. 2007 Jan 15;34(2):509-17. [pdf]

  22. Spring S, Lerch JP, Henkelman RM. Sexual dimorphism revealed in the structure of the mouse brain using three-dimensional magnetic resonance imaging. NeuroImage. 2007 May 1; 35(4):1424-33. [pdf]

  23. Nieman BJ, Lerch JP, Bock NA, Chen XJ, Sled JG, Henkelman RM. Mouse behavioral mutants have neuroimaging abnormalities. Human Brain Mapping. 2007 Jun; 28(6):567-75 [pdf]

  24. Clapcote SJ, Lipina TV, Millar JK, Mackie S, Christie S, Ogawa F, Lerch JP, Trimble K, Uchiyama M, Sakuraba Y, Kaneda H, Shiroishi T, Houslay MD, Henkelman RM, Sled JG, Gondo Y, Porteous DJ, Roder JC. Disc1 missense mutant mice have behavioral and neuroanatomical abnormalities relevant to psychiatric disease. Neuron. 2007 May 3; 54(3):387-402. [pdf]

  25. Nieman NJ, Bishop J, Dazai J, Bock NA, Lerch JP, Feintuch A, Chen XJ, Sled JG, Henkelman RM. MR technology for biological studies in mice. NMR in Biomedicine. 2007 May; 20(3):291-303.

  26. Shaw P, Lerch JP, Pruessner JC, Taylor KN, Rose AB, Greenstein D, Clasen L, Evans A, Rapoport JL, Giedd JN. Cortical morphology in children and adolescents with different apolipoprotein E gene polymorphisms: an observational study. Lancet Neurol. 2007 Jun;6(6):494-500. [pdf]

  27. Shaw P, Gornick M, Lerch J, Addington A, Seal J, Greenstein D, Sharp W, Evans AC, Giedd J, Castellanos FX, Rapoport JL. Polymorphisms of the dopamine D4 receptor, clinical outcome and cortical structure in attention-deficit/ hyperactivity disorder. Archives of Psychiatry. 2007 Aug;64(8):921-31. [pdf]

  28. Lenroot RK, Schmitt JE, Ordaz SJ, Wallace GL, Neale MC, Lerch JP, Kendler KS, Evans AC, Giedd JN. Differences in genetic and environmental influences on the human cerebral cortex associated with development during childhood and adolescence. Human Brain Mapping. 2007 Aug;64(8):921-31. [pdf]

  29. Lerch JP, Carrol JB, Spring S, Bertram LN, Schwab C, Hayden MR, Henkelman RM. Automated deformation analysis in the YAC128 Huntington disease mouse model. NeuroImage. 2008 Jan 1;39(1):32-39. [pdf]

  30. Bohbot VD, Lerch J, Thorndycraft B, Iaria G, Zijdenbos AP. Grey matter differences correlate with spontaneous strategies in a human virtual navigation task. Journal of Neuroscience, 2007 Sep 19;27(38):10078-83. [pdf]

  31. Shaw P, Eckstrand K, Sharp W, Lerch J, Greenstein D, Clasen L, Evans A, Giedd J, Rapoport JL. Attention-deficit/hyperactivity disorder is characterized by a delay in cortical maturation. PNAS, 2007 Dec 4;104(49):19649-54. [pdf]

  32. Hyde KL, Lerch JP, Zatorre RJ, Griffiths TD, Evans AC, Peretz I. Cortical thickness in congenital amusia: when less is better than more. Journal of Neuroscience, 2007 Nov 21;27(47):13028-32. [pdf]

  33. Moro V, Berlucchi G, Lerch J, Tomaiuolo F, Agloti SM. Selective deficit of mental visual imagery with intact primary visual cortex and visual perception. Cortex, 2008 44:109-118. [pdf]

  34. Kale SC, Lerch JP, Henkelman RM, Chen XJ. Optimization of the SNR-resolution tradeoff for registration in magnetic resonance images. Human Brain Mapping. Epub ahead of print, 23 October 2007.

  35. Lerch JP, Carrol JB, Dorr A, Spring S, Hayden M, Sled JG, Henkelman RM. Cortical thickness measured from MRI in the YAC128 mouse model of Huntington’s disease. NeuroImage. Epub ahead of print, 26 Feb. 2008.

  36. Dorr AE, Lerch JP, Spring S, Kabani N, Henkelman RM. High resolution three dimensional brain atlas using an average magnetic resonance image of 40 adult C57BL/6J mice. NeuroImage. Epub ahead of print, 8 Apr. 2008.

  37. Lerch JP, Pruessner J, Zijdenbos AP, Collins DL, Teipel SJ, Hampel H, Evans AC. Automated cortical thickness measurements from MRI can accurately separate Alzheimer's patients from normal elderly controls. Neurobiology of Aging, in Press.

  38. Lenroot RK, Gogtay N, Greenstein DK, Wells EM, Wallace GL, Clasen LS, Blumenthal JD, Lerch J, Zijdenbos AP, Evans AC, Thompson PM, Giedd JN. Sexual dimorphism of brain developmental trajectories during childhood and adolescence. NeuroImage, in Press.

  39. Schmitt JE, Lenroot RK, Wallace GL, Ordaz S, Taylor KN, Kabani N, Greenstein D. Lerch JP, Kendler KS, Neale MC, Giedd JN. Identification of genetically mediated cortical networks: a multivariate study of pediatric twins and siblings. Cerebral Cortex, in Press.

  40. Shaw P, Kabani N, Lerch JP, Eckstrand K, Lenroot R, Gogtay N, Greenstein D, Clasen L, Evans A, Rapoport JL, Giedd JN, Wise SP. Neurodevelopmental trajectories of the human cerebral cortex. Journal of Neuroscience, in Press. [pdf]

  41. Lau JC, Lerch JP, Sled JG, Henkelman RM, Evans AC, Bedell BJ. Longitudinal neuroanatomical changes determined by deformation-based morphometry in mouse models of Alzheimer’s disease. NeuroImage, in Press.

Random stuff

A past poster I presented at the 8th International Conference on Alzheimer's Disease and Related Disorders might also be of interest.

Other than, I'm also occasionally dabbling in more general morphometric analysis - if this interests you, check out the wiki pages at the BIC

This page was last updated April, 2008. For any questions, queries, qualms or concerns email me at