1 % AA_USER_DARTELVBM8 is an AA user script illustrating the preprocessing
   2 % for a voxel-based morphometric analysis, using the "new" segmentation
   3 % introduced in SPM8 and DARTEL registration routines.
   4 %
   5 % As with all AA user scripts, the actual stages of the analysis are
   6 % specified in an XML file - here, in aap_tasklist_dartelvbm8.xml. Although
   7 % pre-defined recipes are distributed with AA, it is easy to modify these
   8 % to suit your needs. You can either save a copy of the same file in your
   9 % matlab path such that it overrides the built-in recipe, or (probably
  10 % more easily) simply save a copy with a new name.
  11 %
  12 % Although the recipe file will set up the stages of analysis and default
  13 % options, additional options can be set for both the overall analysis and
  14 % specific modules.
  15 
  16 clear all
  17 
  18 %% Initialize AA and set basic recipe (aap_tasklist_dartelvbm8.xml)
  19 
  20 aa_ver4_nocloud()
  21 aap = aarecipe('aap_parameters_defaults_CBSU.xml','aap_tasklist_dartelvbm8.xml');
  22 
  23   
  24 %% Set options
  25 aap.options.autoidentifyfieldmaps = 0;
  26 aap.options.autoidentifystructural_chooselast = 1;
  27 aap.options.wheretoprocess = 'qsub'; % parallel; typical localsingle
  28 aap.options.email='All.Knowing@mrc-cbu.cam.ac.uk';
  29 
  30 % Set any other options
  31 aap.tasksettings.aamod_segment8.samp = 2;
  32 
  33 %% Study directory
  34 aap.acq_details.root = '/imaging/xy00/World_Universe_and_Everything';
  35 aap.directory_conventions.analysisid = 'Nature_Paper';
  36 
  37 %% Add subjects
  38 % For many subjects, this can also be scripted to loop through a list.
  39 % cbu
  40 aap = aas_addsubject(aap,90952); 
  41 aap = aas_addsubject(aap,90971);
  42 % camcan
  43 aap = aas_addsubject(aap,110220);
  44 aap = aas_addsubject(aap,110252);
  45     
  46 %% Do the processing
  47 aap = aa_doprocessing(aap);
  48 aas_garbagecollection(aap,true);
  49