SNIPER (Software for Neuro Image Processing)

Faiza Admiraal-Behloul
Roald van der Landen
Baldur van Lew
Julien Milles
Hans Olofsen

Background

This project started officially July the 1st 2002. The development and maintenance phases of brain-O-Matic revealed several software instabilities and limitations in respect to a broader use of the programs for other protocols (such as MTR, ADC or DTI analysis). Indeed, Brain-O-Matic has been made out of existing parts not initially thought and implemented for neuro studies. It was a quick solution for a particular question, and not a long term project. In contrast, SNIPER is a long-term project aimed to the development of stable and multi-platform libraries for neuro-image processing and quantitative analysis. It integrates all the algorithms used in Brain-O-Matic, and more.
SNIPER has a Qt based user interface and 2D image visualization what makes the software platform independent. 3D image visualization is based on VTK (also a platform independent library).

SNIPER includes fully automatic registration and segmentation algorithms and offers a wide variety of editing tools for manual mask drawing or correction of automatically extracted ones: brush, eraser, contour fill in/out, seed point and region growing, and many more (see figure 1).

SNIPER applications What we call application is the bundling of different SNIPER components and wrapping them in a user-friendly graphical interface to be used for a particular purpose. An application is built “à la carte”: The user can specify the sequence of processing steps that he or she would like to perform on a given data set. An interactive wizard is integrated to a GUI to guide the user or the program (in batch mode) through the different steps calling automatically the subsequent segmentation steps , visualization and editing functions. Therefore, a basic GUI has been designed to host different modules for different applications.

Examples of the wide range of studies performed using SNIPER can be found in the publications list.

Status

Ongoing

Gallery

SNIPER-WML
Figure 1. SNIPER-WML

Movie1

Movie2

VentriclesLesions
Automatic brain segmentation and lobe delineation.
To activate the movies (5.0 and 1.0 MB, respectively), please click on the images

Contact

For further information, please contact:
Dr. JR Milles, PhD
Division of Image Processing
Department of Radiology, 1-C2S
Leiden University Medical Center
P.O. Box 9600
2300 RC Leiden
The Netherlands
Tel. +31 (0)71 526 5342
Fax. +31 (0)71 526 6801
mailto: J.R.Milles@lumc.nl

Publications

Journal/Conference Papers

  • Palm WM, Saczynski JS, van der Grond J, Sigurdsson S, Kjartansson O, Jonsson PV, Eiriksdottir G, Gudnason V, Admiraal-Behloul F, Launer LJ and van Buchem MA. “Ventricular dilation: Association with gait and cognition”. Annals of neurology, 66(4):485-493, 2009.
  • Hogers B, van der Weerd L, Olofsen H, van der Graaf LM, DeRuiter MC, Gittenberger-de Groot AC and Poelmann RE. “Non-invasive tracking of avian development in vivo by MRI”. NMR in Biomedicine, 22(4):365-373, 2009.
  • Schmitz N, Admiraal-Behloul F, Arkink EB, Kruit MC, Schoonman GG, Ferrari MD and van Buchem MA. “Attack frequency and disease duration as indicators for brain damage in migraine”. Headache. 48(7):1044-1055, 2008.
  • Schmitz N, Arkink EB, Mulder M, Rubia K, Admiraal-Behloul F, Schoonman GG, Kruit MC, Ferrari MD and van Buchem MA. “Frontal lobe structure and executive function in migraine patients”. Neuroscience Letters. 440(2):92-96, 2008.
  • Moster JP, Admiraal-Behloul F, Hoogduin JM, Luyendijk J, Heersema DJ, van Buchem MA and de Keyser J. “Effects of fluoxetine on disease activity in relapsing multiple sclerosis: a double-blind, placebo-controlled, exploratory study”. Journal of Neurology, Neurosurgery and Psychiatry. 79(9):1027-1031, 2008.
  • van Es AC, van der Grond J, de Craen AJ, Admiraal-Behloul F, Blauw GJ, van Buchem MA. “Risk Factors for Cerebral Microbleeds in the Elderly”. Cerebrovascular Diseases 26(4):397-403, 2008.
  • van Es ACGM, van der Grond J, de Craen AJM, Admiraal-Behloul F, Blauw GJ, van Buchem MA. “Caudate nucleus hypointensity in the elderly is associated with markers of neurodegeneration on MRI”. Neurobiology of Aging. 29(12):1839-1846, 2008.
  • van Es AC, van der Flier WM, Admiraal-Behloul F, Olofsen H, Bollen EL, Middelkoop HA, Weverling-Rijnsburger AW, van der Grond J, Westendorp RG, van Buchem MA. “Lobar Distribution of Changes in Gray Matter and White Matter in Memory Clinic Patients: Detected Using Magnetization Transfer Imaging”. American Journal of Neuroradiology, 28(10):1938-1942, 2007.
  • van den Heuvel DM, ten Dam VH, de Craen AJ, Admiraal-Behloul F, Olofsen H, Bollen EL, Jolles J, Murray HM, Blauw GJ, Westendorp RG, van Buchem MA. “Increase in periventricular white matter hyperintensities parallels decline in mental processing speed in a non-demented elderly population”. Journal of Neurology, Neurosurgery, and Psychiatry. 27(1):76-79, 2006.
  • van den Heuvel DMJ, ten Dam VH, de Craen AJ, Admiraal-Behloul F, van Es AC, Palm WM, Spilt A, Bollen EL, Blauw GJ, Launer L, Westendorp RG, van Buchem MA. “Measuring longitudinal white matter changes: comparison of a visual rating scale with a volumetric measurement”. American Journal of NeuroRadiology, 27(4):875-878, 2006.
  • Tofts PS, Steens SC, Cercignani M, Admiraal-Behloul F, Hofman PA, van Osch MJ, Teeuwisse WM, Tozer DJ, van Waesberghe JH, Yeung R, Barker GJ, van Buchem MA. “Sources of variation in multi-centre brain MTR histogram studies: body-coil transmission eliminates inter-centre differences”. MAGMA. 19(4):209-222, 2006.
  • van Es ACGM, van der Flier WM, Admiraal-Behloul F, Olofsen H, Bollen ELEM, Middelkoop HAM, Weverling-Rijnsburger AWE, Westendorp RGJ, van Buchem MA. “Magnetization transfer imaging of gray and white matter in mild cognitive impairment and Alzheimer's disease”. Neurobiology of Aging. 27(12):1757-1762, 2006.
  • Palm WM, Walchenbach R, Bruinsma B, Admiraal-Behloul F, Middelkoop HA, Launer LJ, van der Grond J, van Buchem MA. “Intracranial compartment volumes in normal pressure hydrocephalus: volumetric assessment versus outcome”. American Journal of NeuroRadiology, 27(1):76-79, 2006.
  • Emmer BJ, Steens SC, Steup-Beekman GM, van der Grond J, Admiraal-Behloul F, Olofsen H, Bosma GP, Ouwendijk WJ, Huizinga TW, van Buchem MA. Detection of change in CNS involvement in neuropsychiatric SLE: a magnetization transfer study. Journal of Magnetic Resonance Imaging. 24(4):812-816, 2006.
  • van den Boom R, Bornebroek M, Behloul F, van den Berg-Huysmans AA, Haan J, van Buchem MA. “Microbleeds in hereditary cerebral hemorrhage with amyloidosis-Dutch type”. Neurology. 64(7):1288-1289, 2005.
  • van der Flier WM, Middelkoop HA, Weverling-Rijnsburger AW, Admiraal-Behloul F, Bollen EL, Westendorp RG, van Buchem MA. “Neuropsychological correlates of MRI measures in the continuum of cognitive decline at old age”. Dementia and Geriatric Cognitive Disorders. 20(2-3):82-88, 2005.
  • Wesselius T, Heersema DJ, Mostert JP, Heerings M, Admiraal-Behloul F, Talebian A, van Buchem MA, De Keyser J. “A randomized crossover study of bee sting therapy for multiple sclerosis”. Neurology. 65(11):1764-1768, 2005.
  • van der Flier WM, van der Vlies AE, Weverling-Rijnsburger AW, de Boer NL, Admiraal-Behloul F, Bollen EL, Westendorp RG, van Buchem MA, Middelkoop HA. “MRI measures and progression of cognitive decline in nondemented elderly attending a memory clinic”. International Journal of Geriatric Psychiatry. 20(11):1060-1066, 2005.
  • Admiraal-Behloul F, van den Heuvel DMJ, Olofsen H, van Osch MJP, van der Grond J, van Buchem MA, Reiber JHC. “Fully automatic segmentation of white matter hyperintensities in MR images of the elderly”. NeuroImage, 28(3):607-617, 2005.
  • Steens SC, Steup-Beekman GM, Bosma GP, Admiraal-Behloul F, Olofsen H, Doornbos J, Huizinga TW, van Buchem MA. The effect of corticosteroid medication on quantitative MR parameters of the brain. American Journal of NeuroRadiology. 26(10):2475-2480, 2005.
  • Steens SC, Admiraal-Behloul F, Schaap JA, Hoogenraad FG, Wheeler-Kingshott CA, le Cessie S, Tofts PS, van Buchem MA. Reproducibility of brain ADC histograms. European Radiology. 14(3):425-430, 2004.
  • van den Heuvel DM, Admiraal-Behloul F, ten Dam VH, Olofsen H, Bollen EL, Murray HM, Blauw GJ, Westendorp RG, de Craen AJ, van Buchem MA. PROSPER Study Group, Different progression rates for deep white matter hyperintensities in elderly men and women. Neurology. 63(9):1699-1701, 2004.
  • Bosma GP, Steens SC, Petropoulos H, Admiraal-Behloul F, van den Haak A, Doornbos J, Huizinga TW, Brooks WM, Harville A, Sibbitt WL Jr, van Buchem MA. Multisequence magnetic resonance imaging study of neuropsychiatric systemic lupus erythematosus. Arthritis & Rheumatism. 50(10):3195-3202, 2004.
  • van der Flier WM, van Buchem MA, Weverling-Rijnsburger AW, Mutsaers ER, Bollen EL, Admiraal-Behloul F, Westendorp RG, Middelkoop HA. Memory complaints in patients with normal cognition are associated with smaller hippocampal volumes. Journal of Neurology. 251(6):671-675, 2004.
  • van der Flier WM, Middelkoop HA, Weverling-Rijnsburger AW, Admiraal-Behloul F, Spilt A, Bollen EL, Westendorp RG, van Buchem MA. Interaction of medial temporal lobe atrophy and white matter hyperintensities in AD. Neurology. 62(10):1862-1864, 2004.
  • Steens SC, Admiraal-Behloul F, Bosma GP, Steup-Beekman GM, Olofsen H, Le Cessie S, Huizinga TW, van Buchem MA. Selective gray matter damage in neuropsychiatric lupus. Arthritis & Rheumatism. 50(9):2877-2881, 2004.
  • van den Boom R, Lesnik Oberstein SA, Split A, Behloul F, Ferrari MD, Haan J, Westendorp RG, van Buchem MA. Cerebral Hemodynamics and White Matter Hyperintensities in CADASIL. Journal of Cerebral Blood Flow & Metabolism. 23(5): 599-604, 2003.

Conference abstracts

  • Mostert IP, Admiraal-Behloul F, Hoogduin IM, Luyetidijk J, Heersema DJ, van Buchem MA, de Keyser J. A randomised, double-blind, placebo-controlled study of fluoxetine for relapsing multiple sclerosis. In: Proceedings ECTRIMS 2007
  • Admiraal-Behloul F, Olofsen H, van den Heuvel DM, Schmitz N, Reiber JH, van Buchem MA. Fully automatic lobe delineation for regional white matter lesion load quantification in a large scale study. In: Proceedings ISMRM 2004.
  • Admiraal-Behloul F, Olofsen H, van den Heuvel DM, van Es AC, Palm WM, Reiber JH, van Buchem MA. Fully automatic white matter lesion load quantification in geriatric subjects. In: Proceedings ISMRM 2004.
  • Steens SC, Admiraal-Behloul F, van Es AC, Steup-Beekman GM, Bosma GP, Olofsen H, Huizinga TW, van Buchem MA. On the effect of oral corticosteroids on magnetization transfer imaging (MTI) measurements. In: Proceedings ISMRM 2004.
  • van den Heuvel DM, van Es AC, ten Dam VH, Palm WM, Admiraal-Behloul F, Spilt A, Blauw G, Bollen EL, Westendorp RG, van Buchem MA. Measuring longitudinal white matter changes: a comparison of a visual rating scale and a quantitative volumetric method. In: Proceedings ISMRM 2004.
  • Schmitz N, Kruit M, Schoonman G, Admiraal-Behloul F, Ferrari M, van Buchem M. Structural abnormalities in migraine, a VBM study. In: Proceedings ISMRM 2004.
  • Admiraal-Behloul F, van den Heuvel D, Schaap J, Olofsen H, Schmitz N, van Buchem MA. Quantification of age-related white matter lesions: a semi-automated method. In: Proceedings ISMRM 2003.
  • Admiraal-Behloul F, van den Heuvel D, Olofsen H, Schmitz N, van Buchem MA. Brain templates for the elderly. In: Proceedings ISMRM 2003.
  • van den Heuvel DM, Admiraal-Behloul F, Olofsen H, Blauw G, Westendorp RG, Bollen EL, Schmitz N, van Buchem MA. Different progression rates for subcortical white matter lesions in healthy elderly males and females. In: Proceedings ISMRM 2003.
  • Steens SCA, Admiraal-Behloul F, Bosma GPT, Huizinga TWJ, van Buchem MA. Involvement of both the gray and white matter in neuropsychiatric systemic lupus erythematosus (NPSLE) as indicated by magnetization transfer imaging (MTI). In: Proceedings ISMRM 2003.
  • Steens SCA, Admiraal-Behloul F, Bosma GPT, Huizinga TWJ, van Buchem MA. Correlation of gray and white matter cerebral lesion load based on volumetric magnetization transfer imaging (MTI) with the presence of antiphospholipid antibodies in neuropsychiatric systemic lupus erythematosus (NP-SLE). In: Proceedings ISMRM 2003.
  • van den Heuvel DMJ, Admiraal-Behloul F, ten Dam VH, Olofsen H, Blauw GJ, Westendorp RG, Bollen ELEM, Schmitz N, van Buchem MA. Different progression rates for subcortical white matter lesions in healthy elderly males and females. In: Proceedings Human Brain Mapping 2003.
  • Admiraal-Behloul F, Schmitz N, van den Heuvel DMJ, Olofsen H, Reiber JHC, van Buchem MA. Geriatric LUMC brain template. In: Proceedings Human Brain Mapping 2003.
  • Steens SCA, Behloul F., Schaap JA, Hoogenraad FGC, Tofts PS, van Buchem MA. Brain ADC histogram parameters depend on b-values and CSF-suppression. In: Proceedings ISMRM 2002.
  • Steens SCA, Behloul F, Schaap JA, Tofts PS, van Buchem MA. ADC histograms - an inter-vendor study. In: Proceedings ISMRM 2002.