Joining data files

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General example

% Example script for batch-processing multiple subjects' Siemens IMA data
% with accompanying water references. Each subject has four scans each to
% be joined together and treated as single datasets during data processing.
% 
% Remember to check GannetPreInitialise.m has the appropriate settings for
% your data: 'join' must be set to '1'.

data_dir = '/Users/username/Documents/my_project/data'; % Root data directory

% For joining files for each subject and batching over multiple subjects, the
% data must be entered as an M x N cell array, where M is the number of
% files per subject and N is the number of subjects. In this example, we
% have only two subjects, each with four files that are to be joined.
sub01 = {'sub-01-1/MPRESS1_1.IMA', ...
         'sub-01-2/MPRESS2_1.IMA', ...
         'sub-01-3/MPRESS3_1.IMA', ...
         'sub-01-4/MPRESS4_1.IMA'};

sub02 = {'sub-02-1/MPRESS1_1.IMA', ...
         'sub-02-2/MPRESS2_1.IMA', ...
         'sub-02-3/MPRESS3_1.IMA', ...
         'sub-02-4/MPRESS4_1.IMA'};

metab_data = [sub01(:), sub02(:)]; % Make an M x N cell array
metab_data = fullfile(data_dir, metab_data); % It is good practice to include the full pathname
         
% Now we do the same for the water reference data. Because of how file
% joining is currently coded in Gannet, there needs to be the same number
% of water reference files per subject as the metabolite data.
sub01_w = {'sub-01-1_w/WATREF1_1.IMA', ...
           'sub-01-2_w/WATREF2_1.IMA', ...
           'sub-01-3_w/WATREF3_1.IMA', ...
           'sub-01-4_w/WATREF4_1.IMA'};

sub02_w = {'sub-02-1_w/WATREF1_1.IMA', ...
           'sub-02-2_w/WATREF2_1.IMA', ...
           'sub-02-3_w/WATREF3_1.IMA', ...
           'sub-02-4_w/WATREF4_1.IMA'};

water_data = [sub01_w(:), sub02_w(:)];
water_data = fullfile(data_dir, water_data);

anat = {'sub-01_T1w.nii', 'sub-02_T1w.nii'};

MRS = GannetLoad(metab_data, water_data);
MRS = GannetFit(MRS);
MRS = GannetCoRegister(MRS, anat);
MRS = GannetSegment(MRS);
MRS = GannetQuantify(MRS);

Siemens RDA files

% Example script for batch-processing multiple subjects' Siemens RDA data
% with accompanying water references. Each subject has two scans each to
% be joined together and treated as single datasets during data processing.
% 
% As Siemens .rda files are typically exported in pairs for MEGA-edited
% data (i.e., edit-ON/edit-OFF subexperiments), the command syntax for
% joining such files is slightly different, as shown below.
%
% Remember to check GannetPreInitialise.m has the appropriate settings for
% your data: 'join' must be set to '1'.

data_dir = '/Users/username/Documents/my_project/data'; % Root data directory

% For joining files for each subject and batching over multiple subjects,
% the data must be entered as an M x N x P cell array, where M is the
% number of files per subject to join, N is the number of subjects, and P
% is the number of subexperiment scans (two for MEGA editing). In this
% example, we have only two subjects, each with two pairs of .rda files
% (two scans) that are to be joined.
fnames_metab = {'sub01_run1_OFF.rda'
                'sub01_run1_ON.rda'
                'sub01_run2_OFF.rda'
                'sub01_run2_ON.rda'
                'sub02_run1_OFF.rda'
                'sub02_run1_ON.rda'
                'sub02_run2_OFF.rda'
                'sub02_run2_ON.rda'};
metab_data(:,1,1) = fnames_metab([1 3]);
metab_data(:,1,2) = fnames_metab([2 4]);
metab_data(:,2,1) = fnames_metab([5 7]);
metab_data(:,2,2) = fnames_metab([6 8]);
metab_data = fullfile(data_dir, metab_data);

% Water reference data are saved as single files. Because of how file
% joining is currently coded in Gannet, there needs to be the same number
% of water reference files per subject as the metabolite data.
fnames_water = {'sub01_water.rda', 'sub02_water.rda'};

water_data(:,1) = fnames_water([1 1]);
water_data(:,2) = fnames_water([2 2]);
water_data = fullfile(data_dir, water_data);

anat = {'sub-01_T1w.nii', 'sub-02_T1w.nii'};

MRS = GannetLoad(metab_data, water_data);
MRS = GannetFit(MRS);
MRS = GannetCoRegister(MRS, anat);
MRS = GannetSegment(MRS);
MRS = GannetQuantify(MRS);

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