run_SiemensMP2RAGErecon.m

% Obviously this needs to point to your data (Siemens MP(2)RAGE with 3D-FatNavs)
rawDataFile = '/home/gallicha/temp/autoTransferTemp/tempRaw/meas_MID36_mp2rage_FN600b_FatNav_06mm.dat';

% And wherever you installed the Retro-MoCo-Box
run('~/Documents/code/retroMoCoBox/addRetroMoCoBoxToPath.m')

% And SPM 12
addpath('~/matlabdownloads/spm12')

% And the Michigan Image Reconstruction Toolbox (MIRT) (http://web.eecs.umich.edu/~fessler/code/) for the NUFFT
run('~/matlabdownloads/mirt/setup.m')

% Set the resolution of the FatNavs that were used (default is 2 for 7T and 4 for 3T)
FatNavRes_mm = 2;

%% Fastest option: if you have loads of RAM (tested with 12 CPUs and 96 Gb of RAM on both 1 mm and 600 um data)

reconstructSiemensMP2RAGEwithFatNavs(rawDataFile,'FatNavRes_mm',FatNavRes_mm,'bGRAPPAinRAM',1,'bKeepReconInRAM',1,'bFullParforRecon',1);

%% if you have plenty of RAM:

% reconstructSiemensMP2RAGEwithFatNavs(rawDataFile,'FatNavRes_mm',FatNavRes_mm,'bGRAPPAinRAM',1);


%% otherwise do the slower version:

% reconstructSiemensMP2RAGEwithFatNavs(rawDataFile,'FatNavRes_mm',FatNavRes_mm,'bGRAPPAinRAM',0);