%% jobSDAT.m
-% This function describes an Osprey job defined in a MATLAB script.
-%
-% A valid Osprey job contains four distinct classes of items:
-% 1. basic information on the MRS sequence used
-% 2. several settings for data handling and modeling
-% 3. a list of MRS (and, optionally, structural imaging) data files
-% to be loaded
-% 4. an output folder to store the results and exported files
-%
-% The list of MRS and structural imaging files is provided in the form of
-% cell arrays. They can simply be provided explicitly, or from a more
-% complex script that automatically determines file names from a given
-% folder structure.
-%
-% Osprey distinguishes between four sets of data:
-% - metabolite (water-suppressed) data
-% (MANDATORY)
-% Defined in cell array "files"
-% - water reference data acquired with the SAME sequence as the
-% metabolite data, just without water suppression RF pulses. This
-% data is used to determine complex coil combination
-% coefficients, and perform eddy current correction.
-% (OPTIONAL)
-% Defined in cell array "files_ref"
-% - additional water data used for water-scaled quantification,
-% usually from short-TE acquisitions due to reduced T2-weighting
-% (OPTIONAL)
-% Defined in cell array "files_w"
-% - Structural image data used for co-registration and tissue class
-% segmentation (usually a T1 MPRAGE). These files need to be
-% provided in the NIfTI format (*.nii or *.nii.gz) or, for GE data, as a
-% folder containing DICOM Files (*.dcm).
-% (OPTIONAL)
-% Defined in cell array "files_nii"
-% - External segmentation results. These files need to be
-% provided in the NIfTI format (*.nii or *.nii.gz).
-% (OPTIONAL)
-% Defined in cell array "files_seg" with 1 x 3 cell for each
-% subject or 1 x 1 cell if a single 4D NIfTI is supplied.
-%
-% Files in the formats
-% - .7 (GE)
-% - .SDAT, .DATA/.LIST, .RAW/.SIN/.LAB (Philips)
-% - .DAT (Siemens)
-% - .nii, .nii.gz (NIfTI-MRS)
-% usually contain all of the acquired data in a single file per scan. GE
-% systems store water reference data in the same .7 file, so there is no
-% need to specify it separately under files_ref.
-%
-% Files in the formats
-% - .DCM (any)
-% - .IMA, .RDA (Siemens)
-% may contain separate files for each average. Instead of providing
-% individual file names, please specify folders. Metabolite data, water
-% reference data, and water data need to be located in separate folders.
-%
-% In the example script at hand the MATLAB functions strrep and which are
-% used to generate a relative path, which allows you to run the examples
-% on your machine directly. To set up your own Osprey job supply the
-% specific locations as described above.
-%
-% AUTHOR:
-% Dr. Georg Oeltzschner (Johns Hopkins University, 2019-07-15)
-% goeltzs1@jhmi.edu
-%
-% HISTORY:
-% 2019-07-15: First version of the code.
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%% 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'}, {'Lac'}, {'PE322'}, {'PE398'} (for 'MEGA')
- % - {'GABA', 'GSH'}, {'GABA', 'Lac'}, {'NAA', 'NAAG'} (for 'HERMES'and 'HERCULES')
-
-
- % Specify data scenario
-dataScenario = 'invivo'; % OPTIONS: - 'invivo' (default)
- % - 'phantom'
- % - 'PRIAM'
- % - 'MRSI'
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%% 2. SPECIFY DATA HANDLING AND MODELING OPTIONS %%%
-% Which spectral registration method should be used? Robust spectral
-% registration is default, a frequency restricted spectral registration
-% method is also availaible and is linked to the fit range.
-opts.SpecReg = 'RobSpecReg'; % OPTIONS: - 'RobSpecReg' (default) Spectral aligment with Water/Lipid removal, using simialrity meric, and weighted averaging
- % - 'ProbSpecReg' Probabilistic spectral aligment to median target and weighted averaging
- % - 'RestrSpecReg' Frequency restricted (fit range) spectral aligment, using simialrity meric, and weighted averaging
- % - 'none'
-
-% Which algorithm do you want to align the sub spectra? L2 norm
-% optimization is the default. This is only used for edited MRS!
-%Perform correction on the metabolite data (raw) or metabolite
-%-nulled data (mm).
-opts.SubSpecAlignment.mets = 'L2Norm'; % OPTIONS: - 'L2Norm' (default)
- % - 'L1Norm'
- % - 'none'
-
-%Perform eddy-current correction on the metabolite data (raw) or metabolite
-%-nulled data (mm). This can either be done similar for all data sets by
-%supplying a single value or specified for each dataset individually by supplying
-% multiple entries (number has to match the number of datasets) e.g. to perform ECC
-% for the second dataset only:
-% opts.ECC.raw = [0 1];
-% opts.ECC.mm = [0 1];
-
-
-opts.ECC.raw = 1; % OPTIONS: - '1' (default)
-opts.ECC.mm = 1; % - '0' (no)
- % - [] array
-
-
-% 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)
-
-% Save processed spectra in NIfTI-MRS format?
-opts.saveNII = 0; % OPTIONS: - 0 (no, default)
- % - 1 (yes)
-
-% Save PDF output for all Osprey modules and subjects?
-opts.savePDF = 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, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
-% Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, 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, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
-opts.fit.includeMetabs = {'default'}; % OPTIONS: - {'default'}
- % - {custom}
-
-% Choose the fitting algorithm
-opts.fit.method = 'Osprey'; % OPTIONS: - 'Osprey' (default)
- % - 'LCModel'
-
-% 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]; % [ppm] Default: [0.5 4]
-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)
-
-% Optional: In case the automatic basisset picker is not working you can manually
-% select the path to the basis set in the osprey/fit/basis, i.e.:
-% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%% 3. SPECIFY MRS DATA AND STRUCTURAL IMAGING FILES %%
-% When using single-average Siemens RDA or DICOM files, specify their
-% folders instead of single files!
-
-% Clear existing files
-clear files files_ref files_w files_nii files_mm
-
-% Data folder in BIDS format
-% The filparts(which()) comment is needed to find the data on your machine. If you set
-% up the jobFile for your own data you can set a direct path to your data
-% folder e.g., data_folder = /Volumes/MyProject/data/'
-
-data_folder = fileparts(which(fullfile('exampledata','sdat','UnEdited','jobSDAT.m')));
-
-% The following lines perform an automated set-up of the jobFile which
-% takes advatage of the BIDS foramt. If you are not using BIDS (highly
-% recommended) you can look at the definitions below the loop to see how to
-% set up direct path links to your data.
-
-subs = dir(data_folder);
-subs(1:2) = [];
-subs = subs([subs.isdir]);
-subs = subs(contains({subs.name},'sub'));
-counter = 1;
-
-for kk = 1:length(subs)
- % Loop over sessions
- sess = dir([subs(kk).folder filesep subs(kk).name]);
- sess(1:2) = [];
- sess = sess([sess.isdir]);
- sess = sess(contains({sess.name},'ses'));
- for ll = 1:length(sess)
-
- % Specify metabolite data
- % (MANDATORY)
- dir_metabolite = dir([sess(ll).folder filesep sess(ll).name filesep 'mrs' filesep subs(kk).name '_' sess(ll).name '_press' filesep '*.SDAT']);
- files(counter) = {[dir_metabolite(end).folder filesep dir_metabolite(end).name]};
-
- % 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.
- dir_ref = dir([sess(ll).folder filesep sess(ll).name filesep 'mrs' filesep subs(kk).name '_' sess(ll).name '_press-ref' filesep '*.SDAT']);
- files_ref(counter) = {[dir_ref(end).folder filesep dir_ref(end).name]};
-
- % Specify water data for quantification (e.g. short-TE water scan)
- % (OPTIONAL)
- files_w = {};
-
- % Specify metabolite-nulled data for quantification
- % (OPTIONAL)
- files_mm = {};
-
- % 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(counter) = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep sess(ll).name '_T1w.nii.gz']};
-
- % External segmentation results
- % (OPTIONAL)
- % Link to NIfTI (*.nii or *.nii.gz) files with segmentation results
- % Add supply gray matter, white matter, and CSF as 1 x 3 cell within a
- % cell array or a single 4D file in the same order supplied as 1 x 1 cell;
-% files_seg(counter) = {{[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep 'c1' sess(ll).name '_T1w.nii.gz'],...
-% [sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep 'c2' sess(ll).name '_T1w.nii.gz'],...
-% [sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep 'c3' sess(ll).name '_T1w.nii.gz']}};
-
-% files_seg(counter) = {{[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep '4D' sess(ll).name '_T1w.nii.gz']}};
-
- counter = counter + 1;
- end
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Definitions without using BIDS
-
-% You can always supply direct path to each of the files within
-% the cell array. For example:
-
-% Specify metabolite data
-% (MANDATORY)
-% files(counter) = {'/Volumes/MyProject/data/sub-01/mrs/PRESS_act.SDAT',...
-% '/Volumes/MyProject/data/sub-02/mrs/PRESS_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(counter) = {'/Volumes/MyProject/data/sub-01/mrs/PRESS_ref.SDAT',...
-% '/Volumes/MyProject/data/sub-02/mrs/PRESS_ref.SDAT'};
-
-% Specify water data for quantification (e.g. short-TE water scan)
-% (OPTIONAL)
-% files_w = {};
-
-% Specify metabolite-nulled data for quantification
-% (OPTIONAL)
-% files_mm = {};
-
-% Specify T1-weighted structural imaging data
-% (OPTIONAL)
-% Link to single NIfTI (*.nii.gz or #.nii) files for GE, Siemens and Philips data
-% files_nii = {'/Volumes/MyProject/data/sub-01/anat/T1w.nii.gz',...
-% '/Volumes/MyProject/data/sub-02/anat/T1w.nii.gz'};
-
-% External segmentation results
-% (OPTIONAL)
-% Link to NIfTI (*.nii or *.nii.gz) files with segmentation results
-% Add supply gray matter, white matter, and CSF as 1 x 3 cell within a
-% cell array or a single 4D file in the same order supplied as 1 x 1 cell;
-% files_seg(counter) = {{'/Volumes/MyProject/data/sub-01/anat/c1T1w.nii.gz',...
-% '/Volumes/MyProject/data/sub-01/anat/c2T1w.nii.gz',...
-% '/Volumes/MyProject/data/sub-01/anat/c3T1w.nii.gz'},...
-% {'/Volumes/MyProject/data/sub-02/anat/c1T1w.nii.gz',...
-% '/Volumes/MyProject/data/sub-02/anat/c2T1w.nii.gz',...
-% '/Volumes/MyProject/data/sub-02/anat/c3T1w.nii.gz'}};
-% files_seg(counter) = {{'/Volumes/MyProject/data/sub-01/anat/4DT1w.nii.gz'},...
-% {'/Volumes/MyProject/data/sub-02/anat/4DT1w.nii.gz'}};
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%% 4. SPECIFY STAT FILE %%%
-% Supply location of a csv file, which contains possible correlation
-% measures and group variables. Each column must start with the name of the
-% measure. For the grouping variable use 'group' and numbers between 1 and
-% the number of included groups. If no group is supplied the data will be
-% treated as one group. (You can always use the direct path)
-
-% file_stat = fullfile(data_folder, 'stat.csv');
-file_stat = '';
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%% 5. 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 (you can always use the direct path)
-% (MANDATORY)
-outputFolder = fullfile(data_folder, 'derivatives');
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% jobSDAT.m
+% This function describes an Osprey job defined in a MATLAB script.
+%
+% A valid Osprey job contains four distinct classes of items:
+% 1. basic information on the MRS sequence used
+% 2. several settings for data handling and modeling
+% 3. a list of MRS (and, optionally, structural imaging) data files
+% to be loaded
+% 4. an output folder to store the results and exported files
+%
+% The list of MRS and structural imaging files is provided in the form of
+% cell arrays. They can simply be provided explicitly, or from a more
+% complex script that automatically determines file names from a given
+% folder structure.
+%
+% Osprey distinguishes between four sets of data:
+% - metabolite (water-suppressed) data
+% (MANDATORY)
+% Defined in cell array "files"
+% - water reference data acquired with the SAME sequence as the
+% metabolite data, just without water suppression RF pulses. This
+% data is used to determine complex coil combination
+% coefficients, and perform eddy current correction.
+% (OPTIONAL)
+% Defined in cell array "files_ref"
+% - additional water data used for water-scaled quantification,
+% usually from short-TE acquisitions due to reduced T2-weighting
+% (OPTIONAL)
+% Defined in cell array "files_w"
+% - Structural image data used for co-registration and tissue class
+% segmentation (usually a T1 MPRAGE). These files need to be
+% provided in the NIfTI format (*.nii or *.nii.gz) or, for GE data, as a
+% folder containing DICOM Files (*.dcm).
+% (OPTIONAL)
+% Defined in cell array "files_nii"
+% - External segmentation results. These files need to be
+% provided in the NIfTI format (*.nii or *.nii.gz).
+% (OPTIONAL)
+% Defined in cell array "files_seg" with 1 x 3 cell for each
+% subject or 1 x 1 cell if a single 4D NIfTI is supplied.
+%
+% Files in the formats
+% - .7 (GE)
+% - .SDAT, .DATA/.LIST, .RAW/.SIN/.LAB (Philips)
+% - .DAT (Siemens)
+% - .nii, .nii.gz (NIfTI-MRS)
+% usually contain all of the acquired data in a single file per scan. GE
+% systems store water reference data in the same .7 file, so there is no
+% need to specify it separately under files_ref.
+%
+% Files in the formats
+% - .DCM (any)
+% - .IMA, .RDA (Siemens)
+% may contain separate files for each average. Instead of providing
+% individual file names, please specify folders. Metabolite data, water
+% reference data, and water data need to be located in separate folders.
+%
+% In the example script at hand the MATLAB functions strrep and which are
+% used to generate a relative path, which allows you to run the examples
+% on your machine directly. To set up your own Osprey job supply the
+% specific locations as described above.
+%
+% AUTHOR:
+% Dr. Georg Oeltzschner (Johns Hopkins University, 2019-07-15)
+% goeltzs1@jhmi.edu
+%
+% HISTORY:
+% 2019-07-15: First version of the code.
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% 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'}, {'Lac'}, {'PE322'}, {'PE398'} (for 'MEGA')
+ % - {'GABA', 'GSH'}, {'GABA', 'Lac'}, {'NAA', 'NAAG'} (for 'HERMES'and 'HERCULES')
+
+
+ % Specify data scenario
+dataScenario = 'invivo'; % OPTIONS: - 'invivo' (default)
+ % - 'phantom'
+ % - 'PRIAM'
+ % - 'MRSI'
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% 2. SPECIFY DATA HANDLING AND MODELING OPTIONS %%%
+% Which spectral registration method should be used? Robust spectral
+% registration is default, a frequency restricted spectral registration
+% method is also availaible and is linked to the fit range.
+opts.SpecReg = 'RobSpecReg'; % OPTIONS: - 'RobSpecReg' (default) Spectral aligment with Water/Lipid removal, using simialrity meric, and weighted averaging
+ % - 'ProbSpecReg' Probabilistic spectral aligment to median target and weighted averaging
+ % - 'RestrSpecReg' Frequency restricted (fit range) spectral aligment, using simialrity meric, and weighted averaging
+ % - 'none'
+
+% Which algorithm do you want to align the sub spectra? L2 norm
+% optimization is the default. This is only used for edited MRS!
+%Perform correction on the metabolite data (raw) or metabolite
+%-nulled data (mm).
+opts.SubSpecAlignment.mets = 'L2Norm'; % OPTIONS: - 'L2Norm' (default)
+ % - 'L1Norm'
+ % - 'none'
+
+%Perform eddy-current correction on the metabolite data (raw) or metabolite
+%-nulled data (mm). This can either be done similar for all data sets by
+%supplying a single value or specified for each dataset individually by supplying
+% multiple entries (number has to match the number of datasets) e.g. to perform ECC
+% for the second dataset only:
+% opts.ECC.raw = [0 1];
+% opts.ECC.mm = [0 1];
+
+
+opts.ECC.raw = 1; % OPTIONS: - '1' (default)
+opts.ECC.mm = 1; % - '0' (no)
+ % - [] array
+
+
+% 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)
+
+% Save processed spectra in NIfTI-MRS format?
+opts.saveNII = 0; % OPTIONS: - 0 (no, default)
+ % - 1 (yes)
+
+% Save PDF output for all Osprey modules and subjects?
+opts.savePDF = 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, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, 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, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+opts.fit.includeMetabs = {'default'}; % OPTIONS: - {'default'}
+ % - {custom}
+
+% Choose the fitting algorithm
+opts.fit.method = 'Osprey'; % OPTIONS: - 'Osprey' (default)
+ % - 'LCModel'
+
+% 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]; % [ppm] Default: [0.5 4]
+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)
+
+% Optional: In case the automatic basisset picker is not working you can manually
+% select the path to the basis set in the osprey/fit/basis, i.e.:
+% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% 3. SPECIFY MRS DATA AND STRUCTURAL IMAGING FILES %%
+% When using single-average Siemens RDA or DICOM files, specify their
+% folders instead of single files!
+
+% Clear existing files
+clear files files_ref files_w files_nii files_mm
+
+% Data folder in BIDS format
+% The filparts(which()) comment is needed to find the data on your machine. If you set
+% up the jobFile for your own data you can set a direct path to your data
+% folder e.g., data_folder = /Volumes/MyProject/data/'
+
+data_folder = fileparts(which(fullfile('exampledata','sdat','UnEdited','jobSDAT.m')));
+
+% The following lines perform an automated set-up of the jobFile which
+% takes advatage of the BIDS foramt. If you are not using BIDS (highly
+% recommended) you can look at the definitions below the loop to see how to
+% set up direct path links to your data.
+
+subs = dir(data_folder);
+subs(1:2) = [];
+subs = subs([subs.isdir]);
+subs = subs(contains({subs.name},'sub'));
+counter = 1;
+
+for kk = 1:length(subs)
+ % Loop over sessions
+ sess = dir([subs(kk).folder filesep subs(kk).name]);
+ sess(1:2) = [];
+ sess = sess([sess.isdir]);
+ sess = sess(contains({sess.name},'ses'));
+ for ll = 1:length(sess)
+
+ % Specify metabolite data
+ % (MANDATORY)
+ dir_metabolite = dir([sess(ll).folder filesep sess(ll).name filesep 'mrs' filesep subs(kk).name '_' sess(ll).name '_press' filesep '*.SDAT']);
+ files(counter) = {[dir_metabolite(end).folder filesep dir_metabolite(end).name]};
+
+ % 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.
+ dir_ref = dir([sess(ll).folder filesep sess(ll).name filesep 'mrs' filesep subs(kk).name '_' sess(ll).name '_press-ref' filesep '*.SDAT']);
+ files_ref(counter) = {[dir_ref(end).folder filesep dir_ref(end).name]};
+
+ % Specify water data for quantification (e.g. short-TE water scan)
+ % (OPTIONAL)
+ files_w = {};
+
+ % Specify metabolite-nulled data for quantification
+ % (OPTIONAL)
+ files_mm = {};
+
+ % 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(counter) = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep sess(ll).name '_T1w.nii.gz']};
+
+ % External segmentation results
+ % (OPTIONAL)
+ % Link to NIfTI (*.nii or *.nii.gz) files with segmentation results
+ % Add supply gray matter, white matter, and CSF as 1 x 3 cell within a
+ % cell array or a single 4D file in the same order supplied as 1 x 1 cell;
+% files_seg(counter) = {{[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep 'c1' sess(ll).name '_T1w.nii.gz'],...
+% [sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep 'c2' sess(ll).name '_T1w.nii.gz'],...
+% [sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep 'c3' sess(ll).name '_T1w.nii.gz']}};
+
+% files_seg(counter) = {{[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep '4D' sess(ll).name '_T1w.nii.gz']}};
+
+ counter = counter + 1;
+ end
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Definitions without using BIDS
+
+% You can always supply direct path to each of the files within
+% the cell array. For example:
+
+% Specify metabolite data
+% (MANDATORY)
+% files(counter) = {'/Volumes/MyProject/data/sub-01/mrs/PRESS_act.SDAT',...
+% '/Volumes/MyProject/data/sub-02/mrs/PRESS_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(counter) = {'/Volumes/MyProject/data/sub-01/mrs/PRESS_ref.SDAT',...
+% '/Volumes/MyProject/data/sub-02/mrs/PRESS_ref.SDAT'};
+
+% Specify water data for quantification (e.g. short-TE water scan)
+% (OPTIONAL)
+% files_w = {};
+
+% Specify metabolite-nulled data for quantification
+% (OPTIONAL)
+% files_mm = {};
+
+% Specify T1-weighted structural imaging data
+% (OPTIONAL)
+% Link to single NIfTI (*.nii.gz or #.nii) files for GE, Siemens and Philips data
+% files_nii = {'/Volumes/MyProject/data/sub-01/anat/T1w.nii.gz',...
+% '/Volumes/MyProject/data/sub-02/anat/T1w.nii.gz'};
+
+% External segmentation results
+% (OPTIONAL)
+% Link to NIfTI (*.nii or *.nii.gz) files with segmentation results
+% Add supply gray matter, white matter, and CSF as 1 x 3 cell within a
+% cell array or a single 4D file in the same order supplied as 1 x 1 cell;
+% files_seg(counter) = {{'/Volumes/MyProject/data/sub-01/anat/c1T1w.nii.gz',...
+% '/Volumes/MyProject/data/sub-01/anat/c2T1w.nii.gz',...
+% '/Volumes/MyProject/data/sub-01/anat/c3T1w.nii.gz'},...
+% {'/Volumes/MyProject/data/sub-02/anat/c1T1w.nii.gz',...
+% '/Volumes/MyProject/data/sub-02/anat/c2T1w.nii.gz',...
+% '/Volumes/MyProject/data/sub-02/anat/c3T1w.nii.gz'}};
+% files_seg(counter) = {{'/Volumes/MyProject/data/sub-01/anat/4DT1w.nii.gz'},...
+% {'/Volumes/MyProject/data/sub-02/anat/4DT1w.nii.gz'}};
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% 4. SPECIFY STAT FILE %%%
+% Supply location of a csv file, which contains possible correlation
+% measures and group variables. Each column must start with the name of the
+% measure. For the grouping variable use 'group' and numbers between 1 and
+% the number of included groups. If no group is supplied the data will be
+% treated as one group. (You can always use the direct path)
+
+% file_stat = fullfile(data_folder, 'stat.csv');
+file_stat = '';
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% 5. 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 (you can always use the direct path)
+% (MANDATORY)
+outputFolder = fullfile(data_folder, 'derivatives');
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
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