.. _scil_gradients_generate_sampling:

scil_gradients_generate_sampling
================================

::

	usage: __main__.py [-h] [--eddy] [--duty]
	                   [--no_b0_start | --b0_every B0_EVERY] [--b0_end]
	                   [--b0_value B0_VALUE] [--b0_philips]
	                   (--bvals bvals [bvals ...] | --b_lin_max B_LIN_MAX | --q_lin_max Q_LIN_MAX)
	                   (--fsl | --mrtrix) [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   nb_samples_per_shell [nb_samples_per_shell ...]
	                   out_basename
	
	Generate multi-shell gradient sampling with various processing options. Helps
	accelerate gradients, optimize duty cycle and avoid artefacts.
	
	Multi-shell gradient sampling is generated as in [1]. The bvecs are then
	flipped to maximize spread for eddy current correction, b0s are interleaved at
	equal spacing and the non-b0 samples are finally shuffled to minimize the total
	diffusion gradient amplitude over a few TR.
	
	-------------------------------------------------------------------------------
	Reference:
	[1] Emmanuel Caruyer, Christophe Lenglet, Guillermo Sapiro,
	    Rachid Deriche. Design of multishell gradient sampling with uniform
	    coverage in diffusion MRI. Magnetic Resonance in Medicine, Wiley, 2013,
	    69 (6), pp. 1534-1540. <http://dx.doi.org/10.1002/mrm.24736>
	-------------------------------------------------------------------------------
	
	positional arguments:
	  nb_samples_per_shell  Number of samples on each non b0 shell. 
	                        If multishell, provide a number per shell.
	  out_basename          Gradient sampling output basename (don't include extension).
	                        Please add options --fsl and/or --mrtrix below.
	
	options:
	  -h, --help            show this help message and exit
	  --eddy                If set, we apply eddy optimization.
	                        B-vectors are flipped to be well spread without symmetry.
	  --duty                If set, we apply duty cycle optimization. 
	                        B-vectors are shuffled to reduce consecutive colinearity in the samples. [False]
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	  -f                    Force overwriting of the output files.
	
	b0 acquisitions:
	  Default if you add no option is to have a b0 at the start.
	
	  --no_b0_start         If set, do not add a b0 at the beginning. 
	  --b0_every B0_EVERY   Interleave a b0 every n=b0_every values. Starts after the first b0 
	                        (cannot be used with --no_b0_start). Must be an integer >= 1.
	  --b0_end              If set, adds a b0 as last sample.
	  --b0_value B0_VALUE   b-value of the b0s. [0.0]
	  --b0_philips          If set, replaces values of b0s bvecs by existing bvecs for Philips handling.
	
	Non-b0 acquisitions:
	  --bvals bvals [bvals ...]
	                        bval of each non-b0 shell.
	  --b_lin_max B_LIN_MAX
	                        b-max for linear bval distribution in *b*.
	  --q_lin_max Q_LIN_MAX
	                        b-max for linear bval distribution in *q*; 
	                        the square root of b-values will be linearly distributed..
	
	Save as:
	  --fsl                 Save in FSL format (.bvec/.bval).
	  --mrtrix              Save in MRtrix format (.b).
	
	2.2.2