BitOfScript - MRC CBU Imaging Wiki

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Type the odd letters out: scieNce GATHeRS knowledge fAster tHAN SOCIeTY GATHErS wisdom

location: BitOfScript

Here is a typical structure for a batch script

  1. {{{Code to set up parameters across all the datasets

and do bits of analysis that are can be grouped }}}

  1. {{{Loop over Subjects and Sessions
  • and perform the Main Crunch

}}}

E.g.

  1. % reorientation, slice timing
    do_time_place5
    realign_spm5
    smooth_spm5
    
    % hp filter
    MYV.hf_cut = 60;
  2. % Run models
    for sb = 1:length(MYV.subjects)
      for ss = 1:length(MYV.sesses)
        one_sub_sess_model_moves5(MYV, sb, ss);
        one_sub_sess_con_moves5(MYV, sb, ss);
      end
    end

Here

  • do_time_place
    realign_spm5
    smooth_spm5
    one_sub_sess_model_moves5
    (OneSubSess)

and

  • one_sub_sess_con_moves5

are subscripts tailored to specialised parts of the sequence.