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.
Can you try removing the “which” and “strrep” parts of the paths you provide? These are really only in the example job files to ensure that they work out of the box, regardless of which folder the user is running Osprey from.