, Volume 58, Issue 11, pp 1153–1160 | Cite as

Basic MR sequence parameters systematically bias automated brain volume estimation

  • Sven HallerEmail author
  • Pavel Falkovskiy
  • Reto Meuli
  • Jean-Philippe Thiran
  • Gunnar Krueger
  • Karl-Olof Lovblad
  • Tobias Kober
  • Alexis Roche
  • Bénédicte Marechal
Functional Neuroradiology



Automated brain MRI morphometry, including hippocampal volumetry for Alzheimer disease, is increasingly recognized as a biomarker. Consequently, a rapidly increasing number of software tools have become available. We tested whether modifications of simple MR protocol parameters typically used in clinical routine systematically bias automated brain MRI segmentation results.


The study was approved by the local ethical committee and included 20 consecutive patients (13 females, mean age 75.8 ± 13.8 years) undergoing clinical brain MRI at 1.5 T for workup of cognitive decline. We compared three 3D T1 magnetization prepared rapid gradient echo (MPRAGE) sequences with the following parameter settings: ADNI-2 1.2 mm iso-voxel, no image filtering, LOCAL− 1.0 mm iso-voxel no image filtering, LOCAL+ 1.0 mm iso-voxel with image edge enhancement. Brain segmentation was performed by two different and established analysis tools, FreeSurfer and MorphoBox, using standard parameters.


Spatial resolution (1.0 versus 1.2 mm iso-voxel) and modification in contrast resulted in relative estimated volume difference of up to 4.28 % (p < 0.001) in cortical gray matter and 4.16 % (p < 0.01) in hippocampus. Image data filtering resulted in estimated volume difference of up to 5.48 % (p < 0.05) in cortical gray matter.


A simple change of MR parameters, notably spatial resolution, contrast, and filtering, may systematically bias results of automated brain MRI morphometry of up to 4–5 %. This is in the same range as early disease-related brain volume alterations, for example, in Alzheimer disease. Automated brain segmentation software packages should therefore require strict MR parameter selection or include compensatory algorithms to avoid MR parameter-related bias of brain morphometry results.


MRI Volumetry Hippocampus 3D T1 



Alzheimer dementia


Alzheimer Disease Neuroimaging Initiative


Cortical gray matter


False discovery rate


Gray matter


Local imaging protocol with 1 mm iso-voxel resolution


Mild cognitive impairment


Magnetization prepared rapid gradient echo


Magnetic resonance imaging


Total intracranial volume


Compliance with ethical standards

We declare that all human and animal studies have been approved by the Geneva University Ethics Committee and have therefore been performed in accordance with the ethical standards laid down in the 1964 Declaration of Helsinki and its later amendments. We declare that the ethics committee waived individual patient consent.

Conflict of interest

TK, BM, GK, and AR are full-time or part-time employees of Siemens Healthcare AG.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Sven Haller
    • 1
    • 2
    Email author
  • Pavel Falkovskiy
    • 3
    • 4
  • Reto Meuli
    • 4
  • Jean-Philippe Thiran
    • 5
  • Gunnar Krueger
    • 6
  • Karl-Olof Lovblad
    • 1
    • 7
  • Tobias Kober
    • 3
    • 5
  • Alexis Roche
    • 3
    • 4
  • Bénédicte Marechal
    • 3
    • 4
  1. 1.Faculty of MedicineUniversity of GenevaGenevaSwitzerland
  2. 2.Affidea Centre de Diagnostique Radiologique de Carouge CDRCGenevaSwitzerland
  3. 3.Advanced Clinical Imaging TechnologySiemens Healthcare HC CEMEA SUI DI BM PILausanneSwitzerland
  4. 4.Department of RadiologyUniversity Hospital (CHUV)LausanneSwitzerland
  5. 5.LTS5, École Polytechnique Fédérale de LausanneLausanneSwitzerland
  6. 6.Siemens Medical Solutions USA, Inc.BostonUSA
  7. 7.University Hospitals of GenevaGenevaSwitzerland

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