Settings example jobfile for twix data (question for edited MRS)

MRS Software Osprey
1

Hi all,

I just noticed there’s an example jobfile in the exampledata>twix folder. However, I see a few differences when comparing it to the one I use, so I have some questions.

In the example twixjobfile there is:

  1. opts.SpecReg = ‘RobSpecReg’;
  2. opts.SubSpecAlignment.mets = ‘L2Norm’;
  3. % opts.ECC.raw = [0 1];
    % opts.ECC.mm = [0 1];

Which I don’t have in my current jobfile (below).

Is adding these to my HERMES/MEGAPRESS/HERCULES jobfile recommended? If yes, what exactly is the input for number 3? I would expect it to be the unsuppressed water scan, so all I have to do is type “1” on both. I got confused by the array option.

My jobfile (for HERMES) is:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% 1. SPECIFY SEQUENCE INFORMATION %%%

% Specify sequence type
seqType = ‘HERMES’; % OPTIONS: - ‘unedited’ (default)
% - ‘MEGA’
% - ‘HERMES’
% - ‘HERCULES’

                            % Specify data scenario

dataScenario = ‘invivo’; % OPTIONS: - ‘invivo’ (default)
% - ‘phantom’

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% 2. SPECIFY DATA HANDLING AND MODELING OPTIONS %%%

% Save LCModel-exportable files for each spectrum?
opts.saveLCM = 0; % OPTIONS: - 0 (no, default)
% - 1 (yes)
% Save jMRUI-exportable files for each spectrum?
opts.saveJMRUI = 0; % OPTIONS: - 0 (no, default)
% - 1 (yes)

% Save processed spectra in vendor-specific format (SDAT/SPAR, RDA, P)?
opts.saveVendor = 0; % OPTIONS: - 0 (no, default)
% - 1 (yes)

% Select the metabolites to be included in the basis set as a cell array,
% with entries separates by commas.
% With default Osprey basis sets, you can select the following metabolites:
% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
% Glu, Gly, H2O, Ins, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, Scyllo, Ser,
% Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
% If you enter ‘default’, the basis set will include all of the above
% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
opts.fit.includeMetabs = {‘default’};

% Choose the fitting algorithm
opts.fit.method = ‘Osprey’; % OPTIONS: - ‘Osprey’ (default)
% - ‘AQSES’ (planned)
% - ‘LCModel’ (planned)
% - ‘TARQUIN’ (planned)

% Choose the fitting style for difference-edited datasets (MEGA, HERMES, HERCULES)
% (only available for the Osprey fitting method)
opts.fit.style = ‘Separate’; % OPTIONS: - ‘Concatenated’ (default) - will fit DIFF and SUM simultaneously)
% - ‘Separate’ - will fit DIFF and OFF separately

% Determine fitting range (in ppm) for the metabolite and water spectra
opts.fit.range = [0.5 4.0]; % [ppm] Default: [0.2 4.2]
opts.fit.rangeWater = [2.0 7.4]; % [ppm] Default: [2.0 7.4]

% Determine the baseline knot spacing (in ppm) for the metabolite spectra
opts.fit.bLineKnotSpace = 0.4; % [ppm] Default: 0.4. (0.55 best for GABA, 0.4 best for GSH: Hupfeld et al 2023 NRM Biomed)

% Add macromolecule and lipid basis functions to the fit?
opts.fit.fitMM = 1; % OPTIONS: - 0 (no)
% - 1 (yes, default)
opts.fit.coMM3 = ‘3to2MM’; % How do you want to model the co-edited macromolecules at 3 ppm for GABA-edited MRS?
% OPTIONS: - {‘3to2MM’} (default)
% - {‘3to2MMsoft’}
% - {‘1to1GABA’}
% - {‘1to1GABAsoft’}
% - {‘freeGauss’}
% - {‘fixedGauss’}
% - {‘none’}
opts.fit.FWHMcoMM3 = 14;

% Which metabolites are edited?
editTarget = {‘GABA’,‘GSH’};

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Thanks,
Andreia

2

Hi @AndreiaPereira,

Osprey will revert to the default settings listed in the example jobfile. In your case:

  1. opts.SpecReg = ‘RobSpecReg’
  2. opts.SubSpecAlignment.mets = ‘L2Norm’
  3. opts.ECC.raw=1

The third options means that it will apply eddy-current correction to all datasets in the container. You only have to add those lines to your jobfile if you want to use different settings than the default. And the brackets for the ECC options are only required if you want to apply eddy-ccurrent correction to a subset of the data in your container which are then indexed by the entries in the array.

Best,
Helge

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