Convert a fixel-based sparse-data image into some form of scalar image
fixel2voxel [ options ] fixel_in operation image_out
- fixel_in: the input fixel data file
- operation: the operation to apply, one of: mean, sum, product, min, max, absmax, magmax, count, complexity, sf, dec_unit, dec_scaled, split_data, split_dir.
- image_out: the output scalar image.
Fixel data can be reduced to voxel data in a number of ways:
- Some statistic computed across all fixel values within a voxel: mean, sum, product, min, max, absmax, magmax
- The number of fixels in each voxel: count
- Some measure of crossing-fibre organisation: complexity, sf (‘single-fibre’)
- A 4D directionally-encoded colour image: dec_unit, dec_scaled
- A 4D scalar image of fixel values with one 3D volume per fixel: split_data
- A 4D image of fixel directions, stored as three 3D volumes per fixel direction: split_dir
- -number N use only the largest N fixels in calculation of the voxel-wise statistic; in the case of “split_data” and “split_dir”, output only the largest N fixels, padding where necessary.
- -weighted fixel_in weight the contribution of each fixel to the per-voxel result according to its volume. E.g. when estimating a voxel-based measure of mean axon diameter, a fixel’s mean axon diameter should be weigthed by its relative volume within the voxel. Note that AFD can be used as a psuedomeasure of fixel volume.
- -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 ‘complexity’ operation:Riffert, T. W.; Schreiber, J.; Anwander, A. & Knosche, T. R. Beyond Fractional Anisotropy: Extraction of bundle-specific structural metrics from crossing fibre models. NeuroImage, 2014, 100, 176-191
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