processFallypride2.m

%% Required setup for Matlab
% ********************* Required ********************
% Notes to execute fslmaths from within Matlab, include the following lines
% in the startup.m file, then run startup.m or restart matlab
% In terminal window run: which fsl to get the install location of fsl
% Example: /usr/local/fsl/bin/fsl ==> fsldir = /usr/local/fsl
% >>edit startup.m
%     fsldir = '/usr/local/fsl';
%     setenv('FSLDIR', fsldir);
%     setenv('PATH',[fsldir, '/etc/matlab:', fsldir, '/bin:', fsldir, '/etc/fslconf:', getenv('PATH')]);
%     % Check http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslEnvironmentVariables
%     setenv('FSLOUTPUTTYPE','NIFTI');
%     clear 'fsldir'
% ***************************************************

%% CMDLINE RUN
% /Applications/MATLAB_R2016b.app/bin/matlab -nodisplay -r "addpath(genpath('/Users/subravcr/Projects/zaldlab-fallypride'));processFallypride2;exit;"
% /usr/local/bin/matlab -nodisplay -r "addpath(genpath('/mnt/teba/Active_Lab_Projects/Chenchal/Code/zaldlab-fallypride'));processFallypride2;exit;"

%% DEFAULT PARAMETER setup block
% default parameters
default_params=@defaultsFallypride;
% Change Default parameters globally for this run
rootDataDir = '/mnt/teba/';
rootAnalysisDir = '/mnt/teba2016/Chenchal/May-02-1/';
% Directory name prefix for each subject: DND005, DND017, etc
subjectDirNamePrefix = 'DND*';
defaults.dataDir = [rootDataDir 'Active_Lab_Projects/DANeuromodulation/PET_Data/Scan/Fallypride/Scan_2/'];
defaults.mriDataDir =[rootDataDir 'Active_Lab_Projects/DANeuromodulation/MRI_Data/DND_Scans/'];
defaults.analysisDir = [rootAnalysisDir 'Fallypride/Scan-2/'];
defaults.realignBaseDir = 'analysis-set';
% Subject's PMOD analysis dir
defaults.pmodAnalysisDir = 'Decay/PMOD_Processed/';
% PMOD nii file [defaults.subject]_Sess1_all_dy.nii
defaults.pmodNiiFileExt = '_Sess2_all_dy.nii';
% PMOD acq times file [defaults.subject]_Sess1.acqtimes
defaults.pmodAcqtimeFileExt ='_Sess2.acqtimes';
defaults.numberOfVols = 35;

%% SUBJECT Block
%% All subjects
allSubjects = dir([defaults.dataDir, subjectDirNamePrefix]);
allSubjects = {allSubjects.name};
subjects = allSubjects;
%% Subject List to override allSubjects
% subjects = {
%     'DND040' 
%     'DND007'
%     };

%% EXCEPTIONS BLOCK to Default parameters per subject
<<<<<<< HEAD
=======
% Exceptions for DND074
DND074.coWipT1Sense = 'DND074_T1.nii';

>>>>>>> release/pet-batch-process-decimal-precision-V1_1
% Exceptions for DND062
DND062.numberOfVols = 34;

% Exceptions for DND072
DND072.coWipT1Sense = 'DND072_T1.nii.gz';
<<<<<<< HEAD
    DND072.brainT1Rois = {
        'cerebellum_T1space.nii'
        'putamen_T1space.nii'
        };
    
=======
DND072.brainT1Rois = {
    'cerebellum_T1space.nii'
    'putamen_T1space.nii'
    };

>>>>>>> release/pet-batch-process-decimal-precision-V1_1
% Exceptions for DND078
DND078.coWipT1Sense = 'DND078_T1.nii.gz';

% Exceptions for DND080
DND080.coWipT1Sense = 'DND080_T1.nii.gz';

<<<<<<< HEAD
% EXAMPLE
% DND005.pmodNiiFileExt = '_Sess1_all_dy.nii';
% DND005.t1Bet=[0 0.6];
% DND005.petBet=[0 0.3 0.4];
% 
% DND005.motionCorrectionRefVol = 'vol0017';
% % [defaults.realignBaseDir]0 will contain analyses with all vols
% DND005.motionCorrectionVolSetsToExclude={
%     {'vol0000'} % Analyses outputs in [defaults.realignBaseDir]1
%     {'vol0000' 'vol0001'} % Analyses outputs in [defaults.realignBaseDir]2
%     {'vol0019' } % Analyses outputs in [defaults.realignBaseDir]2
%     };
=======
>>>>>>> release/pet-batch-process-decimal-precision-V1_1

%% Call for Processing
processPet;