Hi Osprey developers,
I adapted a HERMES jobfile for PRESS analysis. So far I’ve run a few datasets and everything looks fine but could you please let me know whether everything is correctly set up for 35 ms PRESS datasets?
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%%% 1. SPECIFY SEQUENCE INFORMATION %%%
% Specify sequence type
seqType = ‘unedited’; % OPTIONS: - ‘unedited’ (default)
% - ‘MEGA’
% - ‘HERMES’
% - ‘HERCULES’
% Specify data scenario
dataScenario = ‘invivo’; % OPTIONS: - ‘invivo’ (default)
% - ‘phantom’
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%%% 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 4.2]; % [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.
% Add macromolecule and lipid basis functions to the fit?
opts.fit.fitMM = 1; % OPTIONS: - 0 (no)
% - 1 (yes, default)
opts.fit.coMM3 = ‘1to1GABA’;
opts.fit.FWHMcoMM3 = 14;
% Which metabolites are edited?
% editTarget = {‘GABA’,‘GSH’};
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Thank you in advance,
Andreia