diff --git a/spec2nii/Siemens/dicomfunctions.py b/spec2nii/Siemens/dicomfunctions.py index 7e3ad91..8825ca4 100644 --- a/spec2nii/Siemens/dicomfunctions.py +++ b/spec2nii/Siemens/dicomfunctions.py @@ -201,14 +201,16 @@ def not_equal(lst): # Combine data into 5th dimension if needed data_in_gr = data_list[gr] if len(data_in_gr) > 1: - combined_data = np.stack(data_in_gr, axis=-1) + combined_data = np.stack(data_in_gr, axis=-1) + combined_data = np.moveaxis(combined_data, (0, 1, 2, 3, 4), (0, 1, 4, 3, 2)) else: - combined_data = data_in_gr[0] - + combined_data = data_in_gr[0] + # Add dimension information (if not None for default) if tag: meta_used.set_dim_info(0, tag) + # Create NIFTI MRS object. try: nifti_mrs_out.append(gen_nifti_mrs_hdr_ext(combined_data, dt_used, meta_used, or_used.Q44, no_conj=True)) @@ -395,7 +397,7 @@ def process_siemens_csi_vx(img, verbose): # slices = int(xprot[('sSpecPara', 'lFinalMatrixSizeSlice')]) # spectral_points = int(xprot[('sSpecPara', 'lVectorSize')]) - specDataCmplx = specDataCmplx.reshape((slices, rows, cols, spectral_points)) + specDataCmplx = specDataCmplx.reshape((1, rows, cols, spectral_points)) specDataCmplx = np.moveaxis(specDataCmplx, (0, 1, 2), (2, 1, 0)) # 1) Extract dicom parameters