title: Automatic Substitute Computed Tomography Generation and Contouring for Magnetic Resonance Imaging (MRI)-Alone External Beam Radiation Therapy From Standard MRI Sequences.
abstract: OBJECTIVE
  To validate automatic substitute computed tomography CT (sCT) scans generated from standard T2-weighted (T2w) magnetic resonance (MR) pelvic scans for MR-Sim prostate treatment planning.
  
  
  METHODS
  A Siemens Skyra 3T MR imaging (MRI) scanner with laser bridge, flat couch, and pelvic coil mounts was used to scan 39 patients scheduled for external beam radiation therapy for localized prostate cancer. For sCT generation a whole-pelvis MRI scan (1.6 mm 3-dimensional isotropic T2w SPACE [Sampling Perfection with Application optimized Contrasts using different flip angle Evolution] sequence) was acquired. Three additional small field of view scans were acquired: T2w, T2*w, and T1w flip angle 80° for gold fiducials. Patients received a routine planning CT scan. Manual contouring of the prostate, rectum, bladder, and bones was performed independently on the CT and MR scans. Three experienced observers contoured each organ on MRI, allowing interobserver quantification. To generate a training database, each patient CT scan was coregistered to their whole-pelvis T2w using symmetric rigid registration and structure-guided deformable registration. A new multi-atlas local weighted voting method was used to generate automatic contours and sCT results.
  
  
  RESULTS
  The mean error in Hounsfield units between the sCT and corresponding patient CT (within the body contour) was 0.6 ± 14.7 (mean ± 1 SD), with a mean absolute error of 40.5 ± 8.2 Hounsfield units. Automatic contouring results were very close to the expert interobserver level (Dice similarity coefficient): prostate 0.80 ± 0.08, bladder 0.86 ± 0.12, rectum 0.84 ± 0.06, bones 0.91 ± 0.03, and body 1.00 ± 0.003. The change in monitor units between the sCT-based plans relative to the gold standard CT plan for the same dose prescription was found to be 0.3% ± 0.8%. The 3-dimensional γ pass rate was 1.00 ± 0.00 (2 mm/2%).
  
  
  CONCLUSIONS
  The MR-Sim setup and automatic sCT generation methods using standard MR sequences generates realistic contours and electron densities for prostate cancer radiation therapy dose planning and digitally reconstructed radiograph generation.
authors.affiliation: CSIRO Australian e-Health Research Centre, Herston, Queensland, Australia; University of Newcastle, Callaghan, New South Wales, Australia. Electronic address: jason.dowling@csiro.au.
authors.forename: Jason A
authors.initials: JA
authors.lastname: Dowling
authors.affiliation: University of Newcastle, Callaghan, New South Wales, Australia.
authors.forename: Jidi
authors.initials: J
authors.lastname: Sun
authors.affiliation: Calvary Mater Newcastle Hospital, Waratah, New South Wales, Australia.
authors.forename: Peter
authors.initials: P
authors.lastname: Pichler
authors.affiliation: CSIRO Australian e-Health Research Centre, Herston, Queensland, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Rivest-Hénault
authors.affiliation: CSIRO Australian e-Health Research Centre, Herston, Queensland, Australia.
authors.forename: Soumya
authors.initials: S
authors.lastname: Ghose
authors.affiliation: Calvary Mater Newcastle Hospital, Waratah, New South Wales, Australia.
authors.forename: Haylea
authors.initials: H
authors.lastname: Richardson
authors.affiliation: University of Newcastle, Callaghan, New South Wales, Australia; Calvary Mater Newcastle Hospital, Waratah, New South Wales, Australia.
authors.forename: Chris
authors.initials: C
authors.lastname: Wratten
authors.affiliation: University of Newcastle, Callaghan, New South Wales, Australia; Calvary Mater Newcastle Hospital, Waratah, New South Wales, Australia.
authors.forename: Jarad
authors.initials: J
authors.lastname: Martin
authors.affiliation: Calvary Mater Newcastle Hospital, Waratah, New South Wales, Australia.
authors.forename: Jameen
authors.initials: J
authors.lastname: Arm
authors.affiliation: Department of Radiology, Hunter New England Health, New Lambton, New South Wales, Australia.
authors.forename: Leah
authors.initials: L
authors.lastname: Best
authors.affiliation: School of Information Technology and Electrical Engineering, University of Queensland, Brisbane, Queensland, Australia.
authors.forename: Shekhar S
authors.initials: SS
authors.lastname: Chandra
authors.affiliation: CSIRO Australian e-Health Research Centre, Herston, Queensland, Australia.
authors.forename: Jurgen
authors.initials: J
authors.lastname: Fripp
authors.affiliation: University of Newcastle, Callaghan, New South Wales, Australia.
authors.forename: Frederick W
authors.initials: FW
authors.lastname: Menk
authors.affiliation: University of Newcastle, Callaghan, New South Wales, Australia; Calvary Mater Newcastle Hospital, Waratah, New South Wales, Australia.
authors.forename: Peter B
authors.initials: PB
authors.lastname: Greer
mesh_terms: D000368:Aged; D001842:Bone and Bones; D057918:Fiducial Markers; D006046:Gold; D006801:Humans; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D008875:Middle Aged; D064847:Multimodal Imaging / Q000379:methods*; D015588:Observer Variation; D011467:Prostate; D011471:Prostatic Neoplasms / Q000000981:diagnostic imaging / Q000473:pathology / Q000532:radiotherapy*; D011880:Radiotherapy Planning, Computer-Assisted / Q000379:methods*; D061089:Radiotherapy, Image-Guided / Q000379:methods*; D050397:Radiotherapy, Intensity-Modulated; D012007:Rectum; D014057:Tomography, X-Ray Computed / Q000379:methods*; D001743:Urinary Bladder
chemical_list: D006046:Gold