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iCAPs_v2/input_scripts/Inputs_TA_DATA_OpenfMRI.m
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Inputs_TA_DATA_OpenfMRI.m
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%% 1. Parameters to be entered by the user
% General data information
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Path where we have our data stored
param.PathData = 'example data';
% TR of the data
param.TR = 2;
% Links towards the data of all subjects to analyze
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% List of subjects on which to run total activation (must be a cell array
% with all group/subject names). This is where the TA folder will be
% created (or looked for) for each subject
param.Subjects = {'sub-10159','sub-10171'};
% Number of subjects considered
param.n_subjects = length(param.Subjects);
% Title that we wish to give to this specific run of the scripts for saving
% data, or that was used previously for first steps and that we wish to
% build on now
param.title = 'exampleToolbox_openfMRI';
% Information about the folders where to retrieve functional and structural
% data of relevance for the pipeline
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% In all cases, if only one name is given for any variable, the name is
% assumed to be the same across subjects. If there is as many names as
% there is subjects, then the name is assumed to differ across subjects. If
% a [] is provided (e.g. for a folder where to access data), then it is
% assumed that the data lies within the main path itself without any
% additional subpath
% Name of the folder containing the functional data (if void, will directly
% look into the subject folder itself)
param.Folder_functional = 'func/realigned';
param.TA_func_prefix = 's6rf';
% Folder where we can find the probabilistic Gray Matter maps for each
% subject
param.Folder_GM = 'anat/Segmented';
param.TA_gm_prefix = 'c1';
% Information related to GM mask
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Threshold at which we want to threshold the probabilistic gray matter map
% (values larger than this only will be included in the mask); has to lie
% between 0 and 1
param.T_gm = 0.3;
% select if morphological operations (opening and closure) should be
% run on the GM mask to remove wholes, and if yes, specify the size (in
% voxels) for opening and closing operators
param.is_morpho=0;
param.n_morpho_voxels=2;
% Information related to functional preprocessing (skipping scans,
% scubbing, filtering)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Number of scans to discard due to T1 equilibration effects
param.skipped_scans = 5;
% select if detrending should be run on the data, if set to 0 the fields
% 'DCT_TS' and 'Covariates' do not need to be set
param.doDetrend=1;
% Detrending information: cut-off period for the DCT basis (for example,
% 128 means a cutoff of 1/128 = 0.0078 [Hz], and covariates to add (should
% be provided each as a column of 'Covariates')
param.DCT_TS = 128;
param.Covariates = [];
% select if scrubbing should be run on the data, if 0 the fields
% 'Folder_motion', 'TA_mot_prefix', 'skipped_scans_motionfile',
% 'FD_method', 'FD_threshold' and 'interType' do not need to be set
param.doScrubbing=1;
% Folder where motion data from SPM realignment is stored, if motion data
% is taken from another programm than SPM, a text file with the 6 motion
% parameters (3 translational in mm + 3 rotational in rad) should be set as
% input here
param.Folder_motion = param.Folder_functional;
param.TA_mot_prefix = 'rp_f';
% Number of lines to ignore at the beginning of the motion file, if empty
% or not set, this will be equal to param.skipped_scans
param.skipped_scans_motionfile = [];
% Motion information: type of method to use to quantify motion (choose
% between 'Power' and ), and threshold of displacement to use for each
% frame (in [mm])
param.FD_method = 'Power';
param.FD_threshold = 0.5;
% Interpolation method (i.e. 'spline' or 'linear', see interp1 for all
% possibilities) - default (if []) is 'spline'
param.interType='spline';
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