% fmri_initialization initializes color maps, save_directory, image_directory TalairachOutlinesDirectory
global save_directory save_directory_tab statistics_list image_directory TalairachOutlinesDirectory
global  do_zebra fmri_initialization_done max_recursion_depth
if isempty(max_recursion_depth), max_recursion_depth = 50; end
globals
if exist('startup') & isempty(fmri_initialization_done)
	fmri_initialization_done = 1;
	 startup; 
end
MatlabVersion = version;
colmap_setup
if isempty(do_zebra)
	do_zebra = 15;
end
if isempty(save_directory)
	save_directory = '/data1/fmri_data/data/';
end
SetHostid
if isempty(TalairachOutlinesDirectory)
	TalairachOutlinesDirectory = '/data1/fMRIcode/TalairachBlocks/';
end
if isempty(image_directory)
		image_directory = '/data1/fmri_data/images/';
end
statistics_list = [
		'   T_stat      '; 	%  1
	  	'   split-2 T   ';	%  2
		'               ';	%  3
		'mean sig. chang';	%  4
		'  T st. Comb   ';	%  5
		' % difference  ';	%  6
		' % dif. Comb.  ';	%  7
		'   Mann-Whit.  ';	%  8
		'  MW-combined  ';	%  9
		'  pair Tstat   ';	% 10
		'  ROIcorel     ';	% 11
		'  ROIcorel comb';	% 12
		' OnOff BlockCor';	% 13
		' OnOff B.C.comb';	% 14
		' external corel';	% 15
		' ext corel comb';	% 16
		' Total t-stat  ';	% 17
		' mean ON dat   ';	% 18
		' ON st. dev.   ';	% 19
		' Total skew t  ';	% 20
		' Fourier power ';	% 21
		' skew %differ  ';	% 22
		' skew T_stat   ';	% 23
		' skew T/2      ';	% 24
		' t_stat denomin';	% 25
		' skew TmeanCOMB';	% 26
		' skew T comb   ';	% 27
		' skew slope    ';	% 28
		' half & half   ';	% 29
		' neigh. correl.';	% 30
		' gradient X    ';	% 31
		' gradient Y    ';	% 32
		' Fourier phase ';	% 33
		' mean t-stat   ';	% 34
		' ROItab_global ';	% 35
		' T ratio comb  ';	% 36
		' Trat.skew comb';	% 37
		' mixed % dif   ';	% 38
		'               ';	% 39
		' multiple_stat ';	% 40
		' OnStat        ';	% 41
		' OffStat       ';	% 42
		' OnStatSkew    ';	% 43
		' OffStatSkew   ';	% 44
		'Adam''s autocorr';	% 45
		'ROI time_c. tab';	% 46
		'BradStat       ';	% 47
		'Control Stat   ';	% 48
		'ROIcorr_shift  ';	% 49
		'autocor. width ';	% 50
		'Phase Stat     ';	% 51
		'Mean PhaseStat ';	% 52
		'ReneStat       ';	% 53
		'               ';	% 54
		'               ';	% 55
		'               ';	% 56
		'               ';	% 57
		'               ';	% 58
		'               ';	% 59
		'SeriesCoherence';	% 60
		'ROCstat61      ';	% 61
		'ROCstat62      ';	% 62
		'ROCstat63      ';	% 63
		'ROCstat64      ';	% 64
		'ROCstat65      ';	% 65
		'ROCstat66      ';	% 66
		'ROCstat67      ';	% 67
		'ROCstat68      ';	% 68
		'ROCstat69      ';	% 69
		'ROCstat70      ';	% 70
		'               ';	% 71
		'               ';	% 72
		'OnStatSkew     ';	% 73
		'OffStatSkew    ';	% 74
		'               ';	% 75
		'               ';	% 76
		'chris_stat     ';	% 77
		'               ';	% 78
		'               ';	% 79
		'               ';	% 80
		'               ';	% 81
		'               ';	% 82
		'               ';	% 83
		'               ';	% 84
		'               ';	% 85
		'               ';	% 86
		'               ';	% 87
		'               ';	% 88
		'               ';	% 89
		'               ';	% 90
		'               ';	% 91
		'               ';	% 92
		'               ';	% 93
		'               ';	% 94
		'               ';	% 95
		'               ';	% 96
		'               ';	% 97
		'               ';	% 98
		'               ';	% 99
		'               ';	% 100
		];	

if ~isempty(save_directory_tab)
%	 disp('not defining save_directory_tab')
else
save_directory_tab = [	
'/data1/fmri_data/old_data/                                 '; ...
'/data1/mri_group/pawel_data/                               '; ...		
'/data1/mri_group/driesen_data/                             '; ...
'/data1/mri_researchers/jacobsen_data/teenfu/               '; ...
'/data1/mri_researchers/wexler_data/                        '; ...
'/data1/mri_group/chell_data/reading/                       '; ...
'/data1/mri_group/driesen_data/corr/corr_results/           '; ...
'/data1/mri_researchers/pugh_data/results/fmri_data_gonogo/ '; ...
];	
	
a = ['/huey6/naomi/corr/corr_results/            ';		
'/shaun1/zaza/fmri_data_filter/             ';		
'/shaun1/zaza/fmri_data_birdz/              ';
'/shaun1/zaza/fmri_data_fonts/              ';
'/shaun1/zaza/fmri_data_xyz/                ';
'/shaun1/zaza/fmri_data_yufo/               ';
'/boreas1/fmri_data_music/                  ';
'/boreas1/fmri_data_oddball/                ';
'/boreas1/fmri_data_oddvis/                 ';
'/boreas1/fmri_data_rene/fribbles/          ';
'/boreas1/fmri_data_rene/                   ';
'/boreas2/chris_data/                       ';		
'/boreas2/fmri_data_clinical/               ';
'/boreas2/fmri_data_depress/                ';
'/boreas2/fmri_data_glucose/                ';
'/boreas2/fmri_data_leung/                  ';
'/boreas2/fmri_data_math/                   ';
'/boreas2/fmri_data_alison/                 ';
'/rainman1/autism/motion_results/           ';
'/rainman1/autism/motion_results/newNC/     ';
'/rainman1/fmri_data_autism/                ';
'/rainman1/autism/motion_corNewNC/          ';
'/perky1/fmri_data_load/                    ';
'/perky1/fmri_data_szwm/                    ';
'/perky3/fmri_data_emotion/                 ';
'/ketamine1/ayse/fmri_data_vismmn/          ';
'/ketamine1/ayse/fmri_data_numcon/          ';
'/oursun3/fribbles/                         ';
'/oursun3/flankers/                         ';
'/spot5/cheryl/fmri_data_dislexia/          ';
'/spot5/cheryl/fmri_data_dysadult/          ';
'/spot5/cheryl/fmri_data_estrogen/          ';
'/spot5/cheryl/fmri_data_attention/         ';
'/spot5/cheryl/fmri_data_nwr/               ';
'/spot5/cheryl/fmri_data_newdyschild/       ';
'/spot5/cheryl/fmri_data_olddyschild/       ';
'/mistral1/fmri_data_olddyschild_12rerun/   ';
'/spot6/cheryl/fmri_data_alphabet/          ';
'/spot6/cheryl/fmri_data_cls/               ';
'/spot6/cheryl/fmri_data_clslft/            ';
'/spot6/cheryl/fmri_data_einar/             ';
'/spot6/cheryl/fmri_data_estoper/           ';
'/spot6/cheryl/fmri_data_estpilot/          ';
'/spot6/cheryl/fmri_data_estrogen2/         ';
'/spot6/cheryl/fmri_data_loddball/          ';
'/spot6/cheryl/fmri_data_naming/            ';
'/spot6/cheryl/fmri_data_v1study/           ';
'/spot6/cheryl/fmri_data_zulu/              ';
'/spot1/Premies/                            ';
'/spot1/Estroop/                            ';
'/spot1/Eye_Normal/                         ';
'/spot1/Eye_Tourettes/                      ';
'/spot1/Stroop_Normal/                      ';
'/spot1/Stroop_Tourettes/                   ';
'/spot1/Tic_Tourettes/                      ';
'/spot1/Children/                           ';
'/iguana1/fmri_data_leung/                  ';
'/boreas2/fmri_data_leung/new_faceWM/       ';
'/wallace3/alison/results/                  ';
'/wallace2/generate1/results/               ';
'/wallace2/fmri_data_stroke/                ';
'/boreas0/last_fmri_backup/                 ';
'/spot2/fmri_data_estattention              ';
'/feathers1/potenza/                        ';
'/shaun2/data/silvina/                      ';
'/feathers2/gmartino/fmri_data_gmartino/    ';
'/boreas2/fmri_data_leung/new_faceWM/       ';
'/boreas1/fmri_data/                        ';
];
if exist('/home/cheryl/matlab/initialization.mat')
%	load /home/cheryl/matlab/initialization
%	save_directory_tab = [save_directory_tab; start;];
end
end
ReplacementImage = 1;