Clinical Neurology

About NeuRoi

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

NeuRoi is free software, and you are welcome to redistribute it under certain conditions.

Please note:

  1. NeuRoi works on Windows; it has been tested on XP and Vista.
  2. It also seems to work in Linux using WINE.
  3. NeuRoi comes with ABSOLUTELY NO WARRANTY.


Below are some publications that have used NeuRoi:

  • Tench, C. R., R. Tanasescu, C. S. Constantinescu, D. P. Auer and W. J. Cottam "Coordinate Based Random Effect Size meta-analysis of neuroimaging studies." In Press. NeuroImage.

  • Tanasescu, R, Cottam, WJ, Condon, L, Tench, CR, Auer, DP. "Functional reorganisation in chronic pain and neural correlates of pain sensitisation: A coordinate based meta-analysis of 266 cutaneous pain fMRI studies." Neurosci Biobehav Rev 2016.
  • Tench, CR, Tanasescu, R, Auer, DP, Constantinescu, CS. "Coordinate Based Meta-Analysis of Functional Neuroimaging Data; False Discovery Control and Diagnostics." PLOS one 2013
  • Tench CR, Tanasescu R, Auer DP, et al. "Coordinate Based Meta-Analysis of Functional Neuroimaging Data using activation likelihood estimation; Full Width Half Max and group comparisons." PLoS One in press 2014
  • 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.

More publications

  • 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.

Coordinate based Meta-Analysis


NeuRoi can be used to perform coordinate based meta-analysis.

Region of interest analysis


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

  • Semi automated ROIs
  • Manually defined ROIs
  • Statistics/histograms for ROIs

Measuring cervical spinal cord atrophy

NeuRoi spinal cord

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.

Diffusion tensor functions


NeuRoi can perform several DTI functions:

  • Convert diffusion weighted MRI to DTI
  • Convert DTI to scalars: FA, RA, TRACE, eigenvalues
  • 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.  

Other functions

NeuRoi has several other functions to help analyse MRI images:

  • Image coregistration (6 parameter or include scale and shear parameters)
  • Reformat images (change voxel sizes etc.)
  • Image smoothing
  • Inhomogeneity reduction
  • Remove noisy background
  • Extracting the brain using a template
  • Fit T1 relaxation times to inversion recovery images
  • Compute MTR images
  • Histogram Equalisation

Clinical Neurology

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

telephone: +44 (0) 115 823 1441
email:Group Administrator