Hi Guy’s
Trying out Osprey and I don’t seem to be able to get past the “load data” step. When I "click that button in the gui I get this error message:
Array indices must be positive integers or logical values.
Error in OspreyGUIapp (line 320)
gui.layout.RedFileList{i} = [filesep SepFileList{i}{end-2} filesep
SepFileList{i}{end-1} filesep SepFileList{i}{end}];
Error in OspreyStartUp/loadJob (line 131)
OspreyGUIapp(gui.data.MRSCont);
Error in OspreyStartUp/onLoadJob (line 169)
loadJob(gui);
Error while evaluating UIControl Callback.
I’m thinking it’s either something wrong with my job file, or somethign about the data.
The data is a multi-shot (dynamic) SVS PRESS acquisition (48 shots, 8 averages per shot).
The important bits of the job file are below
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% 1. SPECIFY SEQUENCE INFORMATION %%%
% Specify sequence type
seqType = ‘unedited’; % OPTIONS: - ‘unedited’ (default)
% - ‘MEGA’
% - ‘HERMES’
% - ‘HERCULES’
% Specify editing targets
editTarget = {‘none’}; % OPTIONS: - {‘none’} (default if ‘unedited’)
% - {‘GABA’}, {‘GSH’} (for ‘MEGA’)
% - {'GABA, 'GSH}, {‘GABA, GSH, EtOH’} (for ‘HERMES’)
% - {‘HERCULES1’}, {‘HERCULES2’} (for ‘HERCULES’)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% 2. SPECIFY DATA HANDLING AND MODELING OPTIONS %%%
% Save LCModel-exportable files for each spectrum?
opts.saveLCM = 1; % OPTIONS: - 0 (no, default)
% - 1 (yes)
% Save jMRUI-exportable files for each spectrum?
opts.saveJMRUI = 1; % OPTIONS: - 0 (no, default)
% - 1 (yes)
% Save processed spectra in vendor-specific format (SDAT/SPAR, RDA, P)?
opts.saveVendor = 1; % OPTIONS: - 0 (no, default)
% - 1 (yes)
% 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 = [0.2 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)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% 3. SPECIFY MRS DATA AND STRUCTURAL IMAGING FILES %%
% When using single-average Siemens RDA or DICOM files, specify their
% folders instead of single files!
% Specify metabolite data
% (MANDATORY)
files = {which(’/Volumes/Extreme_SSD/SPECTROSCOPY_data/Fingertapping/p02/SS0029_02_WIP_SV_P40_LOC_R1_5_1_raw_act.SDAT’)};
% Specify water reference data for eddy-current correction (same sequence as metabolite data!)
% (OPTIONAL)
% Leave empty for GE P-files (.7) - these include water reference data by
% default.
files_ref = {which(’/Volumes/Extreme_SSD/SPECTROSCOPY_data/Fingertapping/p02/SS0029_02_WIP_SV_P40_LOC_R1_5_1_raw_ref.SDAT’)};
% Specify water data for quantification (e.g. short-TE water scan)
% (OPTIONAL)
files_w = {};
% Specify T1-weighted structural imaging data
% (OPTIONAL)
% Link to single NIfTI (.nii) files for Siemens and Philips data
% Link to DICOM (.dcm) folders for GE data
files_nii = {};
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% 4. SPECIFY OUTPUT FOLDER %%
% The Osprey data container will be saved as a *.mat file in the output
% folder that you specify below. In addition, any exported files (for use
% with jMRUI, TARQUIN, or LCModel) will be saved in sub-folders.
% Specify output folder
% (MANDATORY)
outputFolder = strrep(which(’/Volumes/Extreme_SSD/SPECTROSCOPY_data/Fingertapping/p02/’),‘jobSDAT.m’,‘outputs’);
Any help appreciated.