t_alignInplaneToVolume.m

%% t_alignInplaneToVolume
%
% Illustrates how to align the inplane volume from an fMRI session to the
% 3D volume anatomy using sample data set <erniePRF>
%
% Dependencies: 
%   Remote Data Toolbox
%
% This tutorial is part of a sequence. Run 
%   t_initAnatomyFromFreesurfer
%   t_initVistaSession
% prior to running this tutorial. 
%
% Summary
%
% - Specify alignment matrix linking inplane anatomy to volume anatomy
% - Save mrSESSION with alignment matrix
%
% Tested 07/21/2016 - MATLAB r2015a, Mac OS 10.11.6 
%
%  See also: t_initAnatomyFromFreesurfer t_initVistaSession
%
% Winawer lab (NYU)


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

% Remember where we are
curdir = pwd();

%% Organize functional data

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

% Navigate and create a directory
cd(erniePathTemp)

%% Align inplane to t1 and install Gray/white segmentation

% NOTE: THIS IS A PLACE HOLDER. WE WILL REPLACE THIS WITH CODE THAT SHOWS
% HOW THE ALIGNMENT IS COMPUTED. FOR NOW WE JUST PROVIDE THE ALIGNMENT
% MATRIX.

% navigate and open vistasession
erniePathTemp = fullfile(vistaRootPath, 'local', 'scratch', 'erniePRF');
cd(erniePathTemp)
vw = initHiddenInplane(); % to use the GUI: vw = mrVista;

% aligment matrix (obtained in separate script)
alignMtrx = ...
    1.0e+02 * ...
    [...
    -0.009184260815436  -0.000512038859394   0.007845296072164   2.490305591031722
    0.003943260519177  -0.000392116999562   0.018362671991761   1.307013835970514
    -0.000316306420987   0.009979180755162   0.001124081482535   0.526943057809918
    0                   0                   0   0.010000000000000];

mrSESSION = sessionSet(mrSESSION, 'alignment', alignMtrx);
saveSession();

%% Visualize

% open a 3D volume view
vol = open3ViewWindow('volume');

% Define an ROI that is the entire functional slab
vw = newROI(vw, 'inplane', true);
dataSize = viewGet(vw, 'anat size');
[x, y, z] = ind2sub(dataSize, 1:prod(dataSize));
vw = viewSet(vw, 'ROI coords', [x; y; z]);

% Project this ROI to the volume so that we can see the slice selection
% within the volume
vol = ip2volCurROI(vw ,vol);
vol = refreshScreen(vol, 0);

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