This file contains values (including defaults) for all input parameters to eddy.
# File containing all the images to estimate distortions for
--imain=/autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/dwi_orig_las.nii.gz
# Mask to indicate brain
--mask=/autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb_topup_brain_mask.nii.gz
# File containing indices for all volumes in --imain into --acqp and --topup
--index=/autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/index.txt
# File containing session indices for all volumes in --imain
--session=
# Multi-band factor
--mb=1
# Multi-band offset (-1 if bottom slice removed, 1 if top slice removed)
--mb_offs=0
# Name of text file defining slice/group order
--slorder=
# Name of text file completely specifying slice/group acuistion. N.B. --slspec and --json are mutually exclusive.
--slspec=
# Name of .json text file with information about slice timing. N.B. --json and --slspec are mutually exclusive.
--json=
# Order of slice-to-vol movement model (default 0, i.e. vol-to-vol
--mporder=0
# Regularisation weight for slice-to-vol movement. (default 1, reasonable range 1--10
--s2v_lambda=1
# File containing acquisition parameters
--acqp=/autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/acqp.txt
# Base name for output files from topup
--topup=/autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/topup
# Name of file with susceptibility field (in Hz)
--field=
# Name of rigid body transform for susceptibility field
--field_mat=
# File containing the b-vectors for all volumes in --imain
--bvecs=/autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/dwi_orig_las.bvecs
# File containing the b-values for all volumes in --imain
--bvals=/autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/dwi_orig_las.bvals
# First level EC model (movement/linear/quadratic/cubic, default quadratic)
--flm=quadratic
# Second level EC model (none/linear/quadratic, default none)
--slm=none
# First level EC model for b0 scans (movement/linear/quadratic, default movement)
--b0_flm=movement
# Second level EC model for b0 scans (none/linear/quadratic, default none)
--b0_slm=none
# FWHM for conditioning filter when estimating the parameters (default 0)
--fwhm=0
# FWHM for conditioning filter when estimating slice-to-vol parameters (default 0)
--s2v_fwhm=0
# Number of iterations (default 5)
--niter=5
# Number of iterations for slice-to-vol (default 5)
--s2v_niter=5
# Basename for output
--out=/autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/dwi
# Switch on detailed diagnostic messages (default false)
--very_verbose=False
# Only register the dwi images (default false)
--dwi_only=False
# Only register the b0 images (default false)
--b0_only=False
# Write EC fields as images (default false)
--fields=False
# Write movement induced RMS (deprecated, its use will crash future versions)
--rms=False
# Write total displacement fields (default false)
--dfields=False
# Write shell-wise cnr-maps (default false)
--cnr_maps=False
# Write shell-wise range-cnr-maps (default false)
--range_cnr_maps=False
# Write residuals (between GP and observations), (default false)
--residuals=False
# Write corrected data (additionally) with outliers retained (default false)
--with_outliers=False
# Write history of mss and parameter estimates (default false)
--history=False
# Fill empty planes in x- or y-directions (default false)
--fep=False
# Do not mask output to include only voxels present for all volumes (default false)
--dont_mask_output=False
# Interpolation model for estimation step (spline/trilinear, default spline)
--interp=spline
# Slice-to-vol interpolation model for estimation step (spline/trilinear, default trilinear)
--s2v_interp=trilinear
# Extrapolation model for estimation step (periodic/mirror, default periodic)
--extrap=periodic
# Indicates that extrapolation is valid in EP direction (default false)
--epvalid=False
# Final resampling method (jac/lsr, default jac)
--resamp=jac
# Covariance function for GP (spheri/expo/old, default spheri)
--covfunc=spheri
# Cost-function for GP hyperparameters (MML/CV/GPP/CC, default CV)
--hpcf=CV
# # of voxels used to estimate the hyperparameters (default 1000)
--nvoxhp=1000
# Seeds rand for when selecting voxels (default 0=no seeding)
--initrand=0
# Fudge factor for hyperparameter error variance (default 10.0)
--ff=10
# User specified values for GP hyperparameters
--hypar=
# Write slice-wise stats for each iteration (default false)
--wss=False
# Detect and replace outlier slices (default false))
--repol=False
# Add noise to replaced outliers (default false)
--rep_noise=False
# Number of std off to qualify as outlier (default 4)
--ol_nstd=4
# Min # of voxels in a slice for inclusion in outlier detection (default 250)
--ol_nvox=250
# Error type (1 or 2) to keep constant for outlier detection (default 1)
--ol_ec=1
# Type of outliers, slicewise (sw), groupwise (gw) or both (both). (default sw)
--ol_type=sw
# Consider both positive and negative outliers if set (default false)
--ol_pos=False
# Consider outliers among sums-of-squared differences if set (default false)
--ol_sqr=False
# Estimate how susceptibility field changes with subject movement (default false)
--estimate_move_by_susceptibility=False
# Number of iterations for MBS estimation (default 10)
--mbs_niter=10
# Weighting of regularisation for MBS estimation (default 10)
--mbs_lambda=10
# Knot-spacing for MBS field estimation (default 10mm)
--mbs_ksp=10
# Attempt to separate field offset from subject movement (deprecated, its use will crash future versions)
--sep_offs_move=False
# Do NOT attempt to separate field offset from subject movement (default false)
--dont_sep_offs_move=False
# Second level model for field offset
--offset_model=linear
# Perform a post-eddy alignment of shells (deprecated, its use will crash future versions)
--peas=False
# Do NOT perform a post-eddy alignment of shells (default false)
--dont_peas=False
# Use interspersed b0s to perform post-eddy alignment of shells (default false)
--b0_peas=False
# Assume, don't check, that data is shelled (default false)
--data_is_shelled=True
# Text file with parameters for initialisation
--init=
# Text file with parameters for initialisation of slice-to-vol movement
--init_s2v=
# 4D image file for initialisation of movement-by-susceptibility
--init_mbs=
# Level of debug print-outs (default 0)
--debug=0
# Indicies (zero offset) of volumes for debug print-outs
--dbgindx=
# Regularisation weight for LSR-resampling.
--lsr_lambda=0.01
# Zero-offset # of ref (for location) volume (default 0)
--ref_scan_no=0
# Rotate b-vecs during estimation (default false)
--rbvde=False
# Do a large rotation to test b-vecs
--test_rot=
# Write text file of MI values between shells (default false)
--pmiv=False
# Write text file of (2D) MI values between shells (default false)
--pmip=False
# Write predicted data (in addition to corrected, default false)
--write_predictions=False
# Write predictions obtained with a scattered data approach (in addition to corrected, default false)
--write_scatter_brain_predictions=False
# Write timing information (defaut false)
--log_timings=False
# switch on diagnostic messages
-v,--verbose=False
# display this message
-h,--help=False