Siemens' TWIX reader does not pass voxel dimension to MRSData object

[darrencl]

In the TwixBuilder.build_mrsdata(), the voxel dimension does not seem to be included when constructing the object, nor returned in the parse_twix_header() method.

• TwixBuilder.build_mrsdata()
  

  suspect/suspect/io/twix.py

  Lines 64 to 70 in 86d3c37

  	mrs_data = MRSData(data,
  	self.header_params["dt"],
  	self.header_params["f0"],
  	te=self.header_params["te"],
  	tr=self.header_params["tr"],
  	metadata=metadata,
  	transform=self.header_params["transform"])

• parse_twix_header()
  

  suspect/suspect/io/twix.py

  Lines 284 to 299 in 86d3c37

  	return {"protocol_name": protocol_name,
  	"patient_name": patient_name,
  	"patient_id": patient_id,
  	"patient_birthdate": patient_birthday,
  	"dt": dwell_time,
  	"f0": frequency,
  	"transform": transform,
  	"te": te,
  	"tr": tr,
  	"exam_date": exam_date,
  	"exam_time": exam_time,
  	"sequence_name": sequence_name,
  	"software_version": software_version,
  	"manufacturer": manufacturer,
  	"manufacturers_model_name": manufacturers_model_name
  	}

However, I can see that it is extracted here:

suspect/suspect/io/twix.py

Lines 179 to 197 in 86d3c37

	# get voxel size
	ro_fov_matches = [
	r"sSpecPara\.sVoI\.dReadoutFOV\s*=\s*(-?[[0-9]*[.]?[0-9]*]{0,})\s*",
	r"<ParamDouble.\"VoI_RoFOV\"> { <Precision> \d+( -?[0-9\.]+)? }",
	r"<ParamDouble\.\"VoI_RoFOV\">\s*{\s*(-?[0-9\.]+)?\s*}"
	]
	pe_fov_matches = [
	r"sSpecPara\.sVoI\.dPhaseFOV\s*=\s*(-?[[0-9]*[.]?[0-9]*]{0,})\s*",
	r"<ParamDouble.\"VoI_PeFOV\"> { <Precision> \d+( -?[0-9\.]+)? }",
	r"<ParamDouble\.\"VoI_PeFOV\">\s*{\s*(-?[0-9\.]+)?\s*}"
	]
	slice_thickness_matches = [
	r"sSpecPara\.sVoI\.dThickness\s*=\s*(-?[[0-9]*[.]?[0-9]*]{0,})\s*",
	r"<ParamDouble.\"VoI_SliceThickness\"> { <Precision> \d+( -?[0-9\.]+)? }",
	r"<ParamDouble\.\"VoI_SliceThickness\">\s*{\s*(-?[0-9\.]+)?\s*}"
	]
	ro_fov = get_meta_regex(ro_fov_matches, header_string, default=0)
	pe_fov = get_meta_regex(pe_fov_matches, header_string, default=0)
	slice_thickness = get_meta_regex(slice_thickness_matches, header_string, default=0)

which is then used in transformation_matrix():

suspect/suspect/io/twix.py

Lines 279 to 282 in 86d3c37

	transform = transformation_matrix(row_vector,
	column_vector,
	[pos_sag, pos_cor, pos_tra],
	[ro_fov, pe_fov, slice_thickness])

To confirm, I compared to Siemens' DICOM reader and we can see voxel size/dimension is the last argument of

suspect/suspect/io/siemens.py

Lines 176 to 181 in 02fce7f

	voxel_size = (*csa_header["PixelSpacing"],
	csa_header["SliceThickness"])
	transform = transformation_matrix(row_vector,
	column_vector,
	csa_header["VoiPosition"],
	voxel_size)