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allows to convert 3D CRT MRSI form Vienna #151

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allows to convert 3D CRT MRSI form Vienna #151

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10 changes: 6 additions & 4 deletions spec2nii/Siemens/dicomfunctions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand Down Expand Up @@ -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
Expand Down