diff --git a/scilpy/gradients/bvec_bval_tools.py b/scilpy/gradients/bvec_bval_tools.py index fc4f71983b..faf871559d 100644 --- a/scilpy/gradients/bvec_bval_tools.py +++ b/scilpy/gradients/bvec_bval_tools.py @@ -94,33 +94,33 @@ def check_b0_threshold(min_bval, args): b0_thr = args.b0_threshold if b0_thr > DEFAULT_B0_THRESHOLD: logging.warning( - 'Warning: Your defined b0 threshold (option --{}) is {}. This is ' - 'suspicious. We recommend using volumes with bvalues no higher ' - 'than {} as b0s.'.format(b0_thr, b0_thr, DEFAULT_B0_THRESHOLD)) + 'Your defined b0 threshold is {}. This is suspicious. We ' + 'recommend using volumes with bvalues no higher than {} as b0s' + .format(b0_thr, DEFAULT_B0_THRESHOLD)) if min_bval < 0: logging.warning( 'Warning: Your dataset contains negative b-values (minimal bvalue ' - 'of {}). This is suspicious. We recommend you check your data.') + 'of {}). This is suspicious. We recommend you check your data.' + .format(min_bval)) if min_bval > b0_thr: if args.skip_b0_validation: logging.warning("GOT {} > {}".format(min_bval, b0_thr)) logging.warning( - 'Warning: Your minimal bvalue ({}), is above the threshold ' - 'defined with --{}: {}.\n' - 'Since --skip_b0_validation was specified, the script will' + 'Your minimal bvalue ({}), is above the threshold ({})\n' + 'Since --skip_b0_validation was specified, the script will ' 'proceed with a b0 threshold of {}.' - .format(min_bval, b0_thr, b0_thr, min_bval)) + .format(min_bval, b0_thr, min_bval)) return min_bval else: raise ValueError( - 'The minimal bvalue ({}) is is above the threshold ' - 'defined with --{}: {}.\n.No b0 volumes can be found.\n' + 'The minimal bvalue ({}) is is above the threshold ({})\n' + 'No b0 volumes can be found.\n' 'Please check your data to ensure everything is correct.\n' 'You may also increase the threshold or use ' '--skip_b0_validation' - .format(min_bval, b0_thr, b0_thr, min_bval)) + .format(min_bval, b0_thr)) return b0_thr diff --git a/scilpy/io/btensor.py b/scilpy/io/btensor.py index 16605c3de0..ead25fe9e4 100644 --- a/scilpy/io/btensor.py +++ b/scilpy/io/btensor.py @@ -54,7 +54,9 @@ def generate_btensor_input(in_dwis, in_bvals, in_bvecs, in_bdeltas, """Generate b-tensor input from an ensemble of data, bvals and bvecs files. This generated input is mandatory for all scripts using b-tensor encoding data. Also generate the powder-averaged (PA) data if set. - toDo. Add a way to include a different b0_threshold than the tolerance. + + For the moment, this does not enable the use of a b0_threshold different + than the tolerance. Parameters ---------- diff --git a/scilpy/reconst/frf.py b/scilpy/reconst/frf.py index a8c4d55964..689d5f8598 100644 --- a/scilpy/reconst/frf.py +++ b/scilpy/reconst/frf.py @@ -150,9 +150,14 @@ def compute_msmt_frf(data, bvals, bvecs, btens=None, data_dti=None, 1D bvals array with shape (N,) bvecs : ndarray 2D bvecs array with shape (N, 3) - btens: ? - data_dti: ? - bvals_dti: ? + btens: ndarray 1D + btens array with shape (N,), describing the btensor shape of every + pair of bval/bvec. + data_dti: ndarray 4D + Input diffusion volume with shape (X, Y, Z, M), where M is the number + of DTI directions. + bvals_dti: ndarray 1D + bvals array with shape (M,) bvecs_dti: ? btens_dti: ? mask : ndarray, optional