Test updated version of preproc+QC workflow

[jsheunis]

@lydiatgit

The updated version is available in the lydia branch.

This branch (sitting on top of lcid branch) contains the following updates:

• Improved argument parsing for multiple functions to allow embedding of more bids identifiers, specifically including sessions.
• Adding the fmrwhy_workflow_qc_singleSub workflow to handle the preproc+qc of a single subject separately
• Abstraction of the fmrwhy_workflow_qc_singleSub from `fmrwhy_workflow_qc', where the latter loops through specified subjects in a BIDS dataset and calls the former per subject.
• Adding multiple new options to the settings (via fmrwhy_settings_template), including:
  • options.coreg_type which could be set to per_task, per_run, or to_template
  • Refactoring options.anat_template_session as follows:

% Default behaviour is that session-specific T1w images are used for coregistration of functional
% data in the same session (options.anat_template_session = '')
% Custom behaviour is introduced if a template session is selected (e.g. options.anat_template_session = '1')
% In the latter case the template session T1w image is copied to other sessions (and renamed accordingly)
% in order to simplify processing steps and avoid duplication+overwriting of results. This
% is then followed by the same procedure as session-specific coregistration.
% Copying is only done in the derivatives directory, BIDS dataset data are left untouched.
% This has obvious (possibly bad) implications for interpreting the preprocessed data,
% but it is deemed fine (for now) if we remain aware of this.
options.anat_template_session = '';

TODO:

• the behaviour of the structural-functional coregistration based on options.coreg_type still need to be finalised and tested
• the accompanying behaviour of the realignment also needs to be finalised
• the final step, report generation, needs to be updated to take the above updates into account

[jsheunis]

@lydiatgit you can test the updated workflow as follows:

Overwrite your current fMRwhy code base with the lydia branch.

Then, add the following to your settings file:

options.coreg_type = 'per_task';
options.realignment_type = 'per_task';

Then call the workflow as previously:

fmrwhy_workflow_qc(settings_fn)