Imaging Endpoints


The Buffalo Neuroimaging Analysis Center (BNAC) offers a variety of imaging measures of the brain, spinal cord, and optic nerve for research studies and clinical trials using magnetic resonance imaging (MRI), positron emission tomography (PET), computerized tomography (CT) and magnetic resonance and digital subtraction angiography modalities.


Retrospective studies / re-analysis

Many pre-existing datasets hold valuable information that can now be extracted with newer, more robust image analysis techniques. With state-of-the-art tools like NeuroSTREAM and others, BNAC can quantitatively measure brain atrophy, atrophied lesion volume, thalamic atrophy, and structural dysconnectivity on low-quality, non-standardized, clinical routine images.

See how BNAC can help unlock legacy data

Prospective studies

Selecting and using the correct endpoint(s) for a given trial is vital to ensure that efficacy is not obscured, and to maximize statistical power. BNAC provides guidance in the selection of endpoints and expertise in calculating the most accurate and reproducible data possible.

See individual endpoints


BNAC tools for clinical routine images and legacy datasets

Our newest product is called NeuroSTREAM.  Brain atrophy is a critical component of multiple sclerosis (MS) at all stages of the disease.  Its importance is now widely-recognized and it is becoming a key endpoint in many trials. Early work with the NeuroSTREAM software showed that atrophy is measurable using routine clinical scans.  We have developed and validated a new, robust algorithm for measuring lateral ventricular volume, thalamic volume, atrophied T2-lesion volume, salient central brain ledion volume and dysconnectivity of different brain regions on clinical-quality FLAIR images, an MRI sequence performed as part of most diagnostic and monitoring examinations for MS.  The NeuroSTREAM software offers a user-friendly, cloud-based software platform to remove infrastructure barriers. If you have a need for this service or would like a quote, please contact BNAC.



  • Transfer and storage of MRI scans from various MRI acquisition centers
  • Preprocessing per scan, including: 
    • Image sorting
    • Inhomogeneity correction
    • Noise reduction
    • Conversion of image format
    • Coregistration



  • Calculation of lesion activity (new, enlarging, recurrent, persistent) and scan activity
  • Calculation of old and new ischemic lesions
  • Calculation of number and volume of enhancing lesions
  • Calculation of number and volume of T2 lesions
  • Calculation of number and volume of T1 hypointense lesions
  • Calculation of lesion morphology
  • Calculation of lesion spatial distribution
  • Calculation of lesion histogram matching
  • Calculation of voxel-wise based dynamic lesion changes
  • Vascular and anatomical territorial analysis



  • Calculation of cross-sectional and longitudinal brain atrophy, gray, and white matter atrophy
  • Calculation of regional parenchyma brain atrophy (Freesurfer, VBM)
  • Calculation of regional linear atrophy measures (third ventricular width, bicaudate ratio, lateral ventricular volume, and callosal atrophy)
  • MRI iron measure analysis



  • Calculation of magnetization transfer ratio (MTR) in different tissue compartments



  • Calculation of mean diffusivity
  • Calculation of entropy
  • Calculation of fractional anisotrophy
  • Calculation of axial and radial diffusivity
  • Calculation of free water
  • Calculation of tractography measures



  • Calculation of mean transit time
  • Calculation of cerebral blood flow
  • Calculation of cerebral blood volume



  • Calculation of N-acetyl aspartate
  • Calculation of stem cell peak
  • Calculation of choline
  • Calculation of creatine
  • Calculation of other lipid peaks



  • Record onset times/ behavioral data
  • Processing utilizing SPM software
    • Preprocessing (realignment, slice timing correction, coregistration, normalization and smoothing)
    • Calculation of activated voxels 
      • Individual analyses (scan montages and MNI coordinates) 
      • Group analyses (scan montage and MNI coordinates) 
      • Small Volume Correction (limit analysis to interest areas) 
    • Overlap maps (the summary of binary maps extracted from individual data)
    • Correlational Analyses 
    • Incorporation of phase correction/ field maps 
  • Anatomical labels utilizing Talairach
  • fMRI for purposes of presurgical planning



  • MRI Iron measure analysis
  • Cerebral microbleeds



  • Net Flow
  • Retrograde flow
  • Antegrade flow
  • Peak retrograde velocity
  • Peak antegrade velocity
  • Aqueduct axis length



  • Calculation of number and volume of T2, T1, and GD lesions
  • Calculation of spinal cord atrophy
  • Calculation of magnetization transfer ratio
  • Calculation of spinal cord diffusion measures



  • Calculation of number and volume of T2, T1, and GD lesions
  • Calculation of optic nerve atrophy
  • Calculation of magnetization transfer ratio
  • Calculation of optic nerve diffusion measures (mean diffusivity,fractional anisotropy, and entropy)



  • Internal Jugular Veins
  • CSA measured in upright and supine position
  • ΔCSA calculated difference between supine and upright CSA
  • Velocity measured at point of CSA measurement
  • Vertebral Veins
  • AP diameter measured between cervical processes
  • Velocity measured at point of AP diameter measurement
  • Volume calculation
  • Third Ventricle 
  • Width of third ventricle measured in upright and supine position
  • Calculation of ΔIII Ventricle - difference between supine and upright width
  • Straight Sinus 
  • Velocity measured



  • PET-MRI combined analysis
  • SPECT-MRI combined analysis
  • Development of MRI software programs, web-based programs, and slide animations