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 % 09-12-2013
   8 
   9 %% INITIALISE
  10 clear
  11 
  12 aa_ver4_nocloud
  13 
  14 %% DEFINE SPECIFIC PARAMETERS
  15 %  Default recipe without model
  16 aap=aarecipe('aap_parameters_defaults_CBSU.xml','aap_tasklist_fmri.xml');
  17 
  18 % Modify standard recipe module selection here if you'd like
  19 aap.options.wheretoprocess = 'qsub'; % queuing system			% typical value localsingle
  20 aap.options.autoidentifyfieldmaps=1;  							% typical value 1
  21 aap.options.NIFTI4D = 1;										% typical value 0
  22 aap.options.email='All.Knowing@mrc-cbu.cam.ac.uk';
  23 % Set slice order for slice timing correction
  24 aap.tasksettings.aamod_slicetiming.sliceorder=[32:-1:1];       	% descending
  25 aap.tasksettings.aamod_slicetiming.refslice = 16;              	% reference slice (first acquired)
  26 aap.tasksettings.aamod_firstlevel_model.xBF.UNITS = 'secs';        	% OPTIONS: 'scans'|'secs' for onsets and durations, typical value 'secs'
  27 aap.tasksettings.aamod_firstlevel_model.includemovementpars = 0;% Include/exclude Moco params in/from DM, typical value 1
  28 
  29 %% STUDY
  30 % Directory for analysed data
  31 aap.acq_details.root = '/imaging/xy00/World_Universe_and_Everything'; 
  32 aap.directory_conventions.analysisid = 'Nature_Paper'; 
  33 
  34 % Add data
  35 aap = aas_addsubject(aap,90952,[7]);
  36 aap = aas_addsession(aap,'Loc');
  37 aap = aas_addsubject(aap,90971,[7]);
  38 aap = aas_addsession(aap,'Loc');
  39 
  40 % Add model
  41 % Obtain TR from the first session
  42 h = dicominfo(mri_finddcm(aap, 90952,7));
  43 TR = h.RepetitionTime/1000; % in seconds
  44 
  45 aap = aas_addevent(aap,'aamod_firstlevel_model',mri_findvol(aap,90973),'*',...
  46     'REST',...                                                                                  % name
  47     [30.0560 100.1620 160.2800 200.3700 280.5340 340.6670]-aap.acq_details.numdummies*TR,...    % onsets
  48     [10.0070  10.0230  10.0230  10.0220  10.0210  10.0230]);                                    % durations
  49 aap = aas_addevent(aap,'aamod_firstlevel_model',mri_findvol(aap,90973),'*',...
  50     'RIGHTFINGER',...                                                                           % name
  51     [70.0960 140.2360 170.3030 240.4600 320.6220 350.6890]-aap.acq_details.numdummies*TR,...    % onsets
  52     [10.0220  10.0220  10.0220  10.0220  10.0230  10.0230]);                                    % durations
  53 
  54 aap = aas_addevent(aap,'aamod_firstlevel_model',mri_findvol(aap,90979),'*',...
  55     'REST',...                                                                                  % name
  56     [30.0570 100.1310 160.1990 200.2380 270.3610 330.4300]-aap.acq_details.numdummies*TR,...    % onsets
  57     [10.0070  10.0220  10.0060  10.0220  10.0070  10.0220]);                                    % durations
  58 aap = aas_addevent(aap,'aamod_firstlevel_model',mri_findvol(aap,90979),'*',...
  59     'RIGHTFINGER',...                                                                           % name
  60     [70.0970 140.1860 170.2050 240.3110 310.4020 340.4510]-aap.acq_details.numdummies*TR,...    % onsets
  61     [10.0060  10.0070  10.0210  10.0220  10.0210  10.0220]);                                    % durations
  62 
  63 aap = aas_addcontrast(aap,'aamod_firstlevel_contrasts','*','singlesession:Loc',[-1 1],'Loc_RightFinger-Rest','T');
  64 
  65 %% DO ANALYSIS
  66 aa_doprocessing(aap);
  67 aa_report(fullfile(aas_getstudypath(aap),aap.directory_conventions.analysisid));
  68 aas_garbagecollection(aap,true);