fod2fixel [ options ]  fod
  • fod: the input fod image.


use a fast-marching level-set method to segment fibre orientation distributions, and save parameters of interest as fixel images


  • -mask image only perform computation within the specified binary brain mask image.

Metric values for fixel-based sparse output images

  • -afd image store the total Apparent Fibre Density per fixel (integral of FOD lobe)
  • -peak image store the peak FOD amplitude per fixel
  • -disp image store a measure of dispersion per fixel as the ratio between FOD lobe integral and peak amplitude

FOD FMLS segmenter options

  • -fmls_ratio_integral_to_neg value threshold the ratio between the integral of a positive FOD lobe, and the integral of the largest negative lobe. Any lobe that fails to exceed the integral dictated by this ratio will be discarded. Default: 0.
  • -fmls_ratio_peak_to_mean_neg value threshold the ratio between the peak amplitude of a positive FOD lobe, and the mean peak amplitude of all negative lobes. Any lobe that fails to exceed the peak amplitude dictated by this ratio will be discarded. Default: 1.
  • -fmls_peak_value value threshold the raw peak amplitude of positive FOD lobes. Any lobe for which the peak amplitude is smaller than this threshold will be discarded. Default: 0.1.
  • -fmls_no_thresholds disable all FOD lobe thresholding; every lobe with a positive FOD amplitude will be retained.
  • -fmls_peak_ratio_to_merge value specify the amplitude ratio between a sample and the smallest peak amplitude of the adjoining lobes, above which the lobes will be merged. This is the relative amplitude between the smallest of two adjoining lobes, and the ‘bridge’ between the two lobes. A value of 1.0 will never merge two peaks into a single lobe; a value of 0.0 will always merge lobes unless they are bisected by a zero crossing. Default: 1.

Standard options

  • -info display information messages.
  • -quiet do not display information messages or progress status.
  • -debug display debugging messages.
  • -force force overwrite of output files. Caution: Using the same file as input and output might cause unexpected behaviour.
  • -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading)
  • -failonwarn terminate program if a warning is produced
  • -help display this information page and exit.
  • -version display version information and exit.


  • Reference for the FOD segmentation method:Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT: Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013, 67, 298-312 (Appendix 2)
  • Reference for Apparent Fibre Density:Raffelt, D.; Tournier, J.-D.; Rose, S.; Ridgway, G.R.; Henderson, R.; Crozier, S.; Salvado, O.; Connelly, A. Apparent Fibre Density: a novel measure for the analysis of diffusion-weighted magnetic resonance images.Neuroimage, 2012, 15;59(4), 3976-94.

Author: Robert E. Smith (

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