diff --git a/scripts/dwi_gp_estimation_signal_plot.py b/scripts/dwi_gp_estimation_signal_plot.py index 819ffc7..8005f62 100644 --- a/scripts/dwi_gp_estimation_signal_plot.py +++ b/scripts/dwi_gp_estimation_signal_plot.py @@ -114,7 +114,7 @@ def main() -> None: y_pred = nib.load(args.dwi_pred_data_fname).get_fdata() bvals, bvecs = read_bvals_bvecs(str(args.bval_data_fname), str(args.bvec_data_fname)) - gtab = gradient_table(bvals, bvecs) + gtab = gradient_table(bvals, bvecs=bvecs) # Pick one voxel randomly rng = np.random.default_rng(1234) diff --git a/src/nifreeze/model/_dipy.py b/src/nifreeze/model/_dipy.py index fbf8cbc..b501c8b 100644 --- a/src/nifreeze/model/_dipy.py +++ b/src/nifreeze/model/_dipy.py @@ -286,5 +286,5 @@ def _rasb2dipy(gradient): from dipy.core.gradients import gradient_table warnings.filterwarnings("ignore", category=UserWarning) - retval = gradient_table(gradient[3, :], gradient[:3, :].T) + retval = gradient_table(gradient[3, :], bvecs=gradient[:3, :].T) return retval diff --git a/src/nifreeze/testing/simulations.py b/src/nifreeze/testing/simulations.py index 25ef791..e11b197 100644 --- a/src/nifreeze/testing/simulations.py +++ b/src/nifreeze/testing/simulations.py @@ -178,7 +178,7 @@ def create_single_shell_gradient_table( # Add a b0 value to the gradient table bvals, bvecs = add_b0(bvals, bvecs) - return gradient_table(bvals, bvecs) + return gradient_table(bvals, bvecs=bvecs) def get_query_vectors(