title: Registration of in-vivo to ex-vivo MRI of surgically resected specimens: a pipeline for histology to in-vivo registration.
abstract: BACKGROUND
  Advances in MRI have the potential to improve surgical treatment of epilepsy through improved identification and delineation of lesions. However, validation is currently needed to investigate histopathological correlates of these new imaging techniques. The purpose of this work is to develop and evaluate a protocol for deformable image registration of in-vivo to ex-vivo resected brain specimen MRI. This protocol, in conjunction with our previous work on ex-vivo to histology registration, completes a registration pipeline for histology to in-vivo MRI, enabling voxel-based validation of novel and existing MRI techniques with histopathology.
  
  
  METHODS
  A combination of image-based and landmark-based 3D registration was used to register in-vivo MRI and the ex-vivo MRI from patients (N=10) undergoing epilepsy surgery. Target registration error (TRE) was used to assess accuracy and the added benefit of deformable registration.
  
  
  RESULTS
  A mean TRE of 1.35±0.11 and 1.41±0.33mm was found for neocortical and hippocampal specimens respectively. Statistical analysis confirmed that the deformable registration significantly improved the registration accuracy for both specimens.
  
  
  METHODS
  Image registration of surgically resected brain specimens is a unique application which presents numerous technical challenges and that have not been fully addressed in previous literature. Our computed TRE are comparable to previous attempts tackling similar applications, as registering in-vivo MRI to whole brain or serial histology.
  
  
  CONCLUSIONS
  The presented registration pipeline finds dense and accurate spatial correspondence between in-vivo MRI and histology and allows for the spatially local and quantitative assessment of pathological correlates in MRI.
authors.affiliation: Imaging Research Laboratories, Robarts Research Institute, London, Ontario, Canada; Biomedical Engineering, Western University, London, Ontario, Canada. Electronic address: mgoubran@robarts.ca.
authors.forename: Maged
authors.initials: M
authors.lastname: Goubran
authors.affiliation: Epilepsy Program, Department of Clinical Neurological Sciences, Western University & London Health Sciences Centre, London, Ontario, Canada; Biomedical Engineering, Western University, London, Ontario, Canada.
authors.forename: Sandrine
authors.initials: S
authors.lastname: de Ribaupierre
authors.affiliation: Department of Pathology, Division of Neuropathology, Western University & London Health Sciences Centre, London, Ontario, Canada.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Hammond
authors.affiliation: Imaging Research Laboratories, Robarts Research Institute, London, Ontario, Canada.
authors.forename: Catherine
authors.initials: C
authors.lastname: Currie
authors.affiliation: Epilepsy Program, Department of Clinical Neurological Sciences, Western University & London Health Sciences Centre, London, Ontario, Canada.
authors.forename: Jorge G
authors.initials: JG
authors.lastname: Burneo
authors.affiliation: Epilepsy Program, Department of Clinical Neurological Sciences, Western University & London Health Sciences Centre, London, Ontario, Canada.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Parrent
authors.affiliation: Imaging Research Laboratories, Robarts Research Institute, London, Ontario, Canada; Biomedical Engineering, Western University, London, Ontario, Canada; Department of Medical Biophysics, Western University, London, Ontario, Canada.
authors.forename: Terry M
authors.initials: TM
authors.lastname: Peters
authors.affiliation: Imaging Research Laboratories, Robarts Research Institute, London, Ontario, Canada; Department of Medical Biophysics, Western University, London, Ontario, Canada.
authors.forename: Ali R
authors.initials: AR
authors.lastname: Khan
mesh_terms: D000293:Adolescent; D000328:Adult; D001921:Brain / Q000033:anatomy & histology*; D001931:Brain Mapping / Q000379:methods* / Q000592:standards; D004569:Electroencephalography / Q000379:methods / Q000592:standards; D004833:Epilepsy, Temporal Lobe / Q000175:diagnosis / Q000601:surgery; D005260:Female; D006652:Histological Techniques / Q000379:methods* / Q000592:standards; D006801:Humans; D008279:Magnetic Resonance Imaging / Q000379:methods* / Q000592:standards; D008297:Male; D008875:Middle Aged; D055815:Young Adult
keywords: Anterior temporal lobectomy; Epilepsy; Histology; Image registration; MRI; Pathology