Hello, when I run
[hlhp-105:DANIEL/scripts/2] administrator% $FSLDIR/bin/eddy
I get
***************************************************
The following COMPULSORY options have not been set:
--imain File containing all the images to estimate distortions for
--mask Mask to indicate brain
--index File containing indices for all volumes in --imain into --acqp and --topup
--acqp File containing acquisition parameters
--bvecs File containing the b-vectors for all volumes in --imain
--bvals File containing the b-values for all volumes in --imain
--out Basename for output
***************************************************
Part of FSL (ID: 5.0.11)
eddy
Copyright(c) 2015, University of Oxford (Jesper Andersson)
Usage:
eddy --monsoon
Compulsory arguments (You MUST set one or more of):
--imain File containing all the images to estimate distortions for
--mask Mask to indicate brain
--index File containing indices for all volumes in --imain into --acqp and --topup
--acqp File containing acquisition parameters
--bvecs File containing the b-vectors for all volumes in --imain
--bvals File containing the b-values for all volumes in --imain
--out Basename for output
Optional arguments (You may optionally specify one or more of):
--mb Multi-band factor
--mb_offs Multi-band offset (-1 if bottom slice removed, 1 if top slice removed)
--slspec Name of text file completely specifying slice/group acuistion
--mporder Order of slice-to-vol movement model
--s2v_lambda Regularisation weight for slice-to-vol movement. (default 1, reasonable range 1--10
--topup Base name for output files from topup
--field Name of file with susceptibility field (in Hz)
--field_mat Name of rigid body transform for susceptibility field
--flm First level EC model (movement/linear/quadratic/cubic, default quadratic)
--slm Second level EC model (none/linear/quadratic, default none)
--fwhm FWHM for conditioning filter when estimating the parameters (default 0)
--niter Number of iterations (default 5)
--s2v_niter Number of iterations for slice-to-vol (default 5)
--cnr_maps Write shell-wise cnr-maps
--residuals Write residuals (between GP and observations)
--fep Fill empty planes in x- or y-directions
--interp Interpolation model for estimation step (spline/trilinear, default spline)
--s2v_interp Slice-to-vol interpolation model for estimation step (spline/trilinear, default trilinear)
--resamp Final resampling method (jac/lsr, default jac)
--nvoxhp # of voxels used to estimate the hyperparameters (default 1000)
--initrand Resets rand for when selecting voxels (default false)
--ff Fudge factor for hyperparameter error variance (default 10.0)
--repol Detect and replace outlier slices
--ol_nstd Number of std off to qualify as outlier (default 4)
--ol_nvox Min # of voxels in a slice for inclusion in outlier detection (default 250)
--ol_type Type of outliers, slicewise (sw), groupwise (gw) or both (both). (default sw)
--ol_pos Consider both positive and negative outliers if set (default false)
--ol_sqr Consider outliers among sums-of-squared differences if set (default false)
--dont_sep_offs_move Do NOT attempt to separate field offset from subject movement (default false)
--dont_peas Do NOT perform a post-eddy alignment of shells (default false)
--data_is_shelled Assume, don't check, that data is shelled (default false)
-v,--verbose switch on diagnostic messages
-h,--help display this message
I am running macOS Sierra version 10.12.6
Also, after changing the name of my executable file and trying the different eddy commands I get....
[hlhp-105:DANIEL/scripts/5] administrator% ./script_eddy.sh
subj = AES102 , cond = Rest
eddy: No match.
[hlhp-105:DANIEL/scripts/5] administrator% ./script_eddy.sh
subj = AES102 , cond = Rest
eddy_cuda: No match.
[hlhp-105:DANIEL/scripts/5] administrator% ./script_eddy.sh
subj = AES102 , cond = Rest
eddy_openmp: No match.
Thanks,
Daniel
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