Generate FOD-based DEC maps, with optional panchromatic sharpening and/or luminance/perception correction
fod2dec [ options ] input output
- input: The input FOD image (spherical harmonic coefficients).
- output: The output DEC image (weighted RGB triplets).
By default, the FOD-based DEC is weighted by the integral of the FOD. To weight by another scalar map, use the -contrast option. This option can also be used for panchromatic sharpening, e.g., by supplying a T1 (or other sensible) anatomical volume with a higher spatial resolution.
- -mask image Only perform DEC computation within the specified mask image.
- -contrast image Weight the computed DEC map by the provided image contrast. If the contrast has a different image grid, the DEC map is first resliced and renormalised. To achieve panchromatic sharpening, provide an image with a higher spatial resolution than the input FOD image; e.g., a T1 anatomical volume. Only the DEC is subject to the mask, so as to allow for partial colouring of the contrast image. Default when this option is not provided: integral of input FOD, subject to the same mask/threshold as used for DEC computation.
- -lum Correct for luminance/perception, using default values Cr,Cg,Cb = 0.3,0.5,0.2 and gamma = 2.2 (not correcting is the theoretical equivalent of Cr,Cg,Cb = 1,1,1 and gamma = 2).
- -lum_coefs values The coefficients Cr,Cg,Cb to correct for luminance/perception. Note: this implicitly switches on luminance/perception correction, using a default gamma = 2.2 unless specified otherwise.
- -lum_gamma value The gamma value to correct for luminance/perception. Note: this implicitly switches on luminance/perception correction, using a default Cr,Cg,Cb = 0.3,0.5,0.2 unless specified otherwise.
- -threshold value FOD amplitudes below the threshold value are considered zero.
- -no_weight Do not weight the DEC map; just output the unweighted colours. Reslicing and renormalising of colours will still happen when providing the -contrast option as a template.
- -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.
Dhollander T, Smith RE, Tournier JD, Jeurissen B, Connelly A. Time to move on: an FOD-based DEC map to replace DTI’s trademark DEC FA. Proc Intl Soc Mag Reson Med, 2015, 23, 1027.
Dhollander T, Raffelt D, Smith RE, Connelly A. Panchromatic sharpening of FOD-based DEC maps by structural T1 information. Proc Intl Soc Mag Reson Med, 2015, 23, 566.
Author: Thijs Dhollander (email@example.com)
Copyright: Copyright (C) 2014 The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.