1 % Automatic analysis
   2 % User master script based on
   3 % github.com/rhodricusack/automaticanalysis/wiki/Manual:
   4 % Example (aa version 4.*)
   5 %
   6 % Tibor Auer, MRC-CBSU
   7 % 20-03-2013
   8 
   9 %% INITIALISE
  10 clear
  11 
  12 aa_ver4_nocloud
  13 
  14 %% DEFINE SPECIFIC PARAMETERS
  15 % ANALYSIS RECIPE
  16 %  Default recipe without model
  17 aap=aarecipe('aap_parameters_defaults_CBSU.xml','aap_tasklist_freesurfer.xml');
  18 
  19 % Modify standard recipe module selection here if you'd like
  20 aap.options.wheretoprocess = 'qsub';
  21 aap.options.autoidentifyfieldmaps=0;  % typical value 1
  22 aap.options.email='Tibor.Auer@mrc-cbu.cam.ac.uk';
  23 
  24 %% STUDY
  25 % Directory for analysed data
  26 aap.acq_details.root = '/imaging/ta02/AA';
  27 aap.directory_conventions.analysisid = 'AA_FS';
  28 aap.directory_conventions.continueanalysis = 1;
  29 
  30 % cbu
  31 aap = aas_addsubject(aap,90952); 
  32 aap = aas_addsubject(aap,90971);
  33 % camcan
  34 aap = aas_addsubject(aap,110220);
  35 aap = aas_addsubject(aap,110252);
  36 
  37 %% DO ANALYSIS
  38 aa_doprocessing(aap);
  39 aas_garbagecollection(fullfile(aas_getstudypath(aap),aap.directory_conventions.analysisid),true);
  40 % clear all;