Save in Philips .SDAT file in python

Data Acquisition Philips
1

Hello,

I’m new to MRS Hub and also MRS. Recently I received some data from Philips (.SDAT/.SPAR) and tried to open it using the GannetLoad. However, it didn’t work. This error appeared:

image

Investigating Gannet Software’s PhilipsRead.m code I realized that the problem was related to an odd number of transients in my data (105 transients for for each volunteer). In fact, I tested changing line 24 of the code to the even number (104) and it worked.

24 %MRS_struct.p.nrows(ii) = str2double(sparheader{sparidx+2});
25 MRS_struct.p.nrows(ii) = 104;

But, I wouldn’t want to change PhilipsRead.m I would like to change my data to 104 transients.

So I opened the files using python following this topic: Read in Philips .SDAT/.SPAR files in python. I used these fuctions according to spec2nii/Philips/philips.py:

  • read_sdat()
  • read_spar()
  • _vax_to_ieee_single_float()

My question is in how can I save my changes in .SDAT/.SPAR format? I was able to save the .SPAR file again, but I can’t save it in .SDAT format. Does anyone have any suggestion?

I will be very grateful :slight_smile:

2

Hi @wesna,

I guess that would be something @wclarke could answer.

However, I’m more curious about how you had 105 transients. Are these PRESS data by chance?

Mark

3

Hello @mmikkel,

Yes, in fact this data is MEGA-PRESS.

4

Very odd the number of transients is not even, then. I would double-check your exam card to see if everything is set correctly.

5

This is one of the .SPAR data. Is this enough to double-check?

My idea would be to try changing the value of the ‘rows’ field to 104 and then changing the .SDAT as well.

{'examination_name': 'fMRS-GABA-3freqs',
 'scan_id': 'GABA_MegaPress',
 'scan_date': '2012.03.19 16:42:11',
 'patient_name': '',
 'patient_birth_date': '',
 'patient_position': 'head_first',
 'patient_orientation': 'supine',
 'samples': 2048,
 'rows': 105,
 'synthesizer_frequency': 127770872,
 'offset_frequency': 0,
 'sample_frequency': 2000,
 'echo_nr': 1,
 'mix_number': 1,
 'nucleus': '1H',
 't0_mu1_direction': 0,
 'echo_time': 68,
 'repetition_time': 2000,
 'averages': 8,
 'volume_selection_enable': 'yes',
 'volumes': 1,
 'ap_size': 30,
 'lr_size': 30,
 'cc_size': 30,
 'ap_off_center': 60.34542465,
 'lr_off_center': -5.00035429,
 'cc_off_center': -5.641904354,
 'ap_angulation': 1.679412961,
 'lr_angulation': -38.76796722,
 'cc_angulation': 0.7264128327,
 'volume_selection_method': 1,
 'phase_encoding_enable': 'no',
 't1_measurement_enable': 'no',
 't2_measurement_enable': 'no',
 'time_series_enable': 'no',
 'image_plane_slice_thickness': 0,
 'slice_distance': 0,
 'nr_of_slices_for_multislice': 1,
 'Spec.image in plane transf': 'plusA-plusB',
 'spec_data_type': 'cf',
 'spec_sample_extension': '[V]',
 'spec_num_col': 2048,
 'spec_col_lower_val': -1000,
 'spec_col_upper_val': -998.9760132,
 'spec_col_extension': '[sec]',
 'spec_num_row': 105,
 'spec_row_lower_val': 1,
 'spec_row_upper_val': 105,
 'spec_row_extension': '[index]',
 'num_dimensions': 2,
 'dim1_ext': '[sec]',
 'dim1_pnts': 2048,
 'dim1_low_val': -1000,
 'dim1_step': 0.0005000000237,
 'dim1_direction': 'mu1',
 'dim1_t0_point': 0,
 'dim2_ext': '[num]',
 'dim2_pnts': 1,
 'dim2_low_val': 1.0,
 'dim2_step': 1.0,
 'dim2_direction': 'x',
 'dim2_t0_point': 50,
 'dim3_ext': '[num]',
 'dim3_pnts': 1,
 'dim3_low_val': 1.0,
 'dim3_step': 1.0,
 'dim3_direction': 'y',
 'dim3_t0_point': 50,
 'echo_acquisition': 'ECHO',
 'TSI_factor': 0,
 'spectrum_echo_time': 68,
 'spectrum_inversion_time': 0,
 'image_chemical_shift': 0,
 'resp_motion_comp_technique': 'NONE',
 'de_coupling': 'NO',
 'equipment_sw_verions': '2.6.3 ; .6.3 ;',
 'placeholder1': None,
 'placeholder2': None}
6

Better to check the parameters as saved on your scanner.

7

Unfortunately, this is not within my reach. The data was only shared with me. I wasn’t the one who made the acquisitions :slightly_frowning_face:

8

I would suggest consulting with whoever provided the data and asking about the acquisition parameters.