.. _fod2fixel:

fod2fixel
===================

Synopsis
--------

Perform segmentation of continuous Fibre Orientation Distributions (FODs) to produce discrete fixels

Usage
--------

::

    fod2fixel [ options ]  fod fixel_directory

-  *fod*: the input fod image.
-  *fixel_directory*: the output fixel directory

Options
-------

Metric values for fixel-based sparse output images
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-afd image** output the total Apparent Fibre Density per fixel (integral of FOD lobe)

-  **-peak image** output the peak FOD amplitude per fixel

-  **-disp image** output a measure of dispersion per fixel as the ratio between FOD lobe integral and peak amplitude

FOD FMLS segmenter options
^^^^^^^^^^^^^^^^^^^^^^^^^^

-  **-fmls_integral value** threshold absolute numerical integral of positive FOD lobes. Any lobe for which the integral is smaller than this threshold will be discarded. Default: 0.

-  **-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.

Other options for fod2fixel
^^^^^^^^^^^^^^^^^^^^^^^^^^^

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

-  **-maxnum number** maximum number of fixels to output for any particular voxel (default: no limit)

-  **-nii** output the directions and index file in nii format (instead of the default mif)

-  **-dirpeak** define the fixel direction as the peak lobe direction as opposed to the lobe mean

Standard options
^^^^^^^^^^^^^^^^

-  **-info** display information messages.

-  **-quiet** do not display information messages or progress status. Alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.

-  **-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).

-  **-help** display this information page and exit.

-  **-version** display version information and exit.

References
^^^^^^^^^^

* 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 (AFD):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 (robert.smith@florey.edu.au)

**Copyright:** Copyright (c) 2008-2018 the MRtrix3 contributors.

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