t_initVistaSession.m

%% t_initVistaSession
%
% Illustrates how to initialize a mrVista session with functional MRI data
% using sample data set <erniePRF>
%
% Dependencies: 
%   Remote Data Toolbox
%
% This tutorial is part of a sequence. Run 
%   t_initAnatomyFromFreesurfer
% prior to running this tutorial. 
%
% Summary
%
% - Download <erniePRF> sample data set
% - Create new folder, and move EPI and inplane files there
% - Specify session parameters
% - Initialize and visualize
%
% Tested 07/21/2016 - MATLAB r2015a, Mac OS 10.11.6 
%
%  See also: t_initAnatomyFromFreesurfer
%
% Winawer lab (NYU)


%% Download ernie raw MRI data

% Clean start in case we have a vista session open
mrvCleanWorkspace();

% Remember where we are
curdir = pwd();

% If we find the directory, do not bother unzipping again
forceOverwrite = false; 

% Get it
erniePRFOrig = mrtInstallSampleData('functional', 'erniePRF', [], forceOverwrite);


%% Organize functional data

% Create a new directory in 'scratch' for the tutorial
erniePathTemp = fullfile(vistaRootPath, 'local', 'scratch', 'erniePRF');

% make directory
mkdir(erniePathTemp)

% Navigate and create a directory
cd(erniePathTemp)

% Set up Raw data file directory
mkdir Raw;

% These are the EPI and inplane files downloaded with the pRF sample data
fname{1} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI01.nii.gz');
fname{2} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI02.nii.gz');
fname{3} = fullfile(erniePRFOrig, 'Raw', 'Ernie_EPI03.nii.gz');
fname{4} = fullfile(erniePRFOrig, 'Raw', 'ErnieInplane.nii.gz');

% Move the files from the downloaded directory to the new, clear directory
for ii = 1:length(fname)
    copyfile(fname{ii}, fullfile(erniePathTemp, 'Raw'));    
end

%% Initialize a vistasoft session

% These files have been copied to the scratch directory. Use local paths.
epiFile{1}     = fullfile('Raw','Ernie_EPI01.nii.gz');
epiFile{2}     = fullfile('Raw','Ernie_EPI02.nii.gz');
epiFile{3}     = fullfile('Raw','Ernie_EPI03.nii.gz');
inplaneFile    = fullfile('Raw','ErnieInplane.nii.gz'); 
anatFile       = fullfile('3DAnatomy', 't1.nii.gz');

% Generate the expected generic params structure
params = mrInitDefaultParams;

% And insert the required parameters: 
params.inplane      = inplaneFile; 
params.functionals  = epiFile; 
params.sessionDir   = erniePathTemp; 

% Specify some optional parameters
%       3D volume anatomy (originally from freesurfer)
params.vAnatomy     = anatFile;
%       Drop the first 8 volumes in each scan, keep remaining volumes
params.keepFrames   = [8 -1; 8 -1; 8 -1]; 
%       Subject ID. For most labs, it is probably safest to use an
%       anonymized coding scheme
params.subject      = 'Ernie';
%       Name for each of the three scans
params.annotations = {'PRF 1', 'PRF 2', 'PRF 3'};

% Do the initialization: 
ok = mrInit(params); 

% Open a graphical user interface to ensure that we succeeded
vw = mrVista('inplane');

%% Clean up
close(viewGet(vw, 'figure number')); 
mrvCleanWorkspace
cd(curdir)