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NeuRoi Image analysis software

NeuRoititle

NeuRoi is locally developed software for processing MRI images. It will work with Analyze and some Nifti images.

A few of the publications that have used NeuRoi:

  • Dineen, RA, Vilisaar, J, Hlinka, J, et al. (2009). "Disconnection as a mechanism for cognitive dysfunction in multiple sclerosis." Brain 132 (Pt 1): 239-49.
  • Mann, RS, Constantinescu, CS and Tench, CR (2007). "Upper cervical spinal cord cross-sectional area in relapsing remitting multiple sclerosis: application of a new technique for measuring cross-sectional area on magnetic resonance images." J Magn Reson Imaging 26 (1): 61-5.
  • Niepel, G, Tench CR, Morgan, PS, et al. (2006). "Deep gray matter and fatigue in MS: a T1 relaxation time study." J Neurol 253 (7): 896-902.
  • Zellini, F, Niepel, G, Tench, CR, et al. (2009). "Hypothalamic involvement assessed by T1 relaxation time in patients with relapsing-remitting multiple sclerosis." Mult Scler 15 (12): 1442-9.

  

NeuRoi works on windows; it has been tested on XP and Vista.

*It also seems to work in Linux using WINE.

download1

 

Region of interest analysis Neuroi1

 NeuRoi can be used to perform region of interest (ROI) analysis.

      N Semi automated ROIs

      N Manually defined ROIs

      N Statistics/histograms for ROIs  

 

 

 

 

 

 

 

 

Measuring cervical spinal cord atrophy 

NeuRoi can be used to measure upper cervical cord atrophy with a correction for partial volume. The function incorporated is detailed in:

  • Tench, CR, Morgan, PS and Constantinescu, CS (2005). "Measurement of cervical spinal cord cross-sectional area by MRI using edge detection and partial volume correction." J Magn Reson Imaging 21 (3): 197-203.

 

NeuRoiCord

 

 

Diffusion tensor functions 

NeuRoi can perform several DTI functions:

      N Convert diffusion weighted MRI to DTI

      N Convert DTI to scalars: FA, RA, TRACE, eigenvalues

      N Use tractography to extract specific fibre tracts, as detailed in:

  • Tench, CR, Morgan, PS, Wilson, M, et al. (2002). "White matter mapping using diffusion tensor MRI." Magn ResonMed  47 (5): 967-72.

 

tractography

 

Other functions 

NeuRoi has several other functions to help analyse MRI images:

     N Image coregistration (6 parameter or include scale and shear parameters)

     N Reformat images (change voxel sizes etc.)

     N Image smoothing

     N Inhomogeneity reduction

     N Remove noisy background

     N Extracting the brain using a template

     N Fit T1 relaxation times to inversion recovery images

     N  Compute MTR images

     N  Histogram Equalisation

     N  Phase unwrapping

 

Clinical Neurology

University of Nottingham
C Floor, South Block
Queen's Medical Centre
Nottingham
NG7 2UH

telephone: +44 (0) 115 823 1441
fax: +44 (0) 115 970 9738
email: nicola.thomas@nottingham.ac.uk