use of a mask

[Haris Styliadis]

Dear experts, 

I have tried to run a previously used script for GLMFlex for a 2x2x2 ANOVA

I have noticed that though I expect the results to be within a specified mask, the specified mask does not have any effect on the results. I have tried various masks

Following is the script

Scans = {

'r1_sub_01_av_cc_cc_HV.img'

'r1_sub_01_av_cc_cc_LV.img'

'r1_sub_01_av_cc_cc_zHA.img'

'r1_sub_01_av_cc_cc_zLA.img'

'r1_sub_02_av_cc_cc_HV.img'

'r1_sub_02_av_cc_cc_LV.img'

'r1_sub_02_av_cc_cc_zHA.img'

'r1_sub_02_av_cc_cc_zLA.img'

'r1_sub_03_av_cc_cc_HV.img'

'r1_sub_03_av_cc_cc_LV.img'

'r1_sub_03_av_cc_cc_zHA.img'

'r1_sub_03_av_cc_cc_zLA.img'

'r1_sub_04_av_cc_cc_HV.img'

'r1_sub_04_av_cc_cc_LV.img'

'r1_sub_04_av_cc_cc_zHA.img'

'r1_sub_04_av_cc_cc_zLA.img'

'r1_sub_05_av_cc_cc_HV.img'

'r1_sub_05_av_cc_cc_LV.img'

'r1_sub_05_av_cc_cc_zHA.img'

'r1_sub_05_av_cc_cc_zLA.img'

'r1_sub_06_av_cc_cc_HV.img'

'r1_sub_06_av_cc_cc_LV.img'

'r1_sub_06_av_cc_cc_zHA.img'

'r1_sub_06_av_cc_cc_zLA.img'

'r1_sub_07_av_cc_cc_HV.img'

'r1_sub_07_av_cc_cc_LV.img'

'r1_sub_07_av_cc_cc_zHA.img'

'r1_sub_07_av_cc_cc_zLA.img'

'r1_sub_08_av_cc_cc_HV.img'

'r1_sub_08_av_cc_cc_LV.img'

'r1_sub_08_av_cc_cc_zHA.img'

'r1_sub_08_av_cc_cc_zLA.img'

'r1_sub_09_av_cc_cc_HV.img'

'r1_sub_09_av_cc_cc_LV.img'

'r1_sub_09_av_cc_cc_zHA.img'

'r1_sub_09_av_cc_cc_zLA.img'

'r1_sub_10_av_cc_cc_HV.img'

'r1_sub_10_av_cc_cc_LV.img'

'r1_sub_10_av_cc_cc_zHA.img'

'r1_sub_10_av_cc_cc_zLA.img'

'r1_sub_11_av_cc_cc_HV.img'

'r1_sub_11_av_cc_cc_LV.img'

'r1_sub_11_av_cc_cc_zHA.img'

'r1_sub_11_av_cc_cc_zLA.img'

'r1_sub_12_av_cc_cc_HV.img'

'r1_sub_12_av_cc_cc_LV.img'

'r1_sub_12_av_cc_cc_zHA.img'

'r1_sub_12_av_cc_cc_zLA.img'

'r2_sub_01_av_cc_cc_HV.img'

'r2_sub_01_av_cc_cc_LV.img'

'r2_sub_01_av_cc_cc_zHA.img'

'r2_sub_01_av_cc_cc_zLA.img'

'r2_sub_02_av_cc_cc_HV.img'

'r2_sub_02_av_cc_cc_LV.img'

'r2_sub_02_av_cc_cc_zHA.img'

'r2_sub_02_av_cc_cc_zLA.img'

'r2_sub_03_av_cc_cc_HV.img'

'r2_sub_03_av_cc_cc_LV.img'

'r2_sub_03_av_cc_cc_zHA.img'

'r2_sub_03_av_cc_cc_zLA.img'

'r2_sub_04_av_cc_cc_HV.img'

'r2_sub_04_av_cc_cc_LV.img'

'r2_sub_04_av_cc_cc_zHA.img'

'r2_sub_04_av_cc_cc_zLA.img'

'r2_sub_05_av_cc_cc_HV.img'

'r2_sub_05_av_cc_cc_LV.img'

'r2_sub_05_av_cc_cc_zHA.img'

'r2_sub_05_av_cc_cc_zLA.img'

'r2_sub_06_av_cc_cc_HV.img'

'r2_sub_06_av_cc_cc_LV.img'

'r2_sub_06_av_cc_cc_zHA.img'

'r2_sub_06_av_cc_cc_zLA.img'

'r2_sub_07_av_cc_cc_HV.img'

'r2_sub_07_av_cc_cc_LV.img'

'r2_sub_07_av_cc_cc_zHA.img'

'r2_sub_07_av_cc_cc_zLA.img'

'r2_sub_08_av_cc_cc_HV.img'

'r2_sub_08_av_cc_cc_LV.img'

'r2_sub_08_av_cc_cc_zHA.img'

'r2_sub_08_av_cc_cc_zLA.img'

'r2_sub_09_av_cc_cc_HV.img'

'r2_sub_09_av_cc_cc_LV.img'

'r2_sub_09_av_cc_cc_zHA.img'

'r2_sub_09_av_cc_cc_zLA.img'

'r2_sub_10_av_cc_cc_HV.img'

'r2_sub_10_av_cc_cc_LV.img'

'r2_sub_10_av_cc_cc_zHA.img'

'r2_sub_10_av_cc_cc_zLA.img'

'r2_sub_11_av_cc_cc_HV.img'

'r2_sub_11_av_cc_cc_LV.img'

'r2_sub_11_av_cc_cc_zHA.img'

'r2_sub_11_av_cc_cc_zLA.img'

'r2_sub_12_av_cc_cc_HV.img'

'r2_sub_12_av_cc_cc_LV.img'

'r2_sub_12_av_cc_cc_zHA.img'

'r2_sub_12_av_cc_cc_zLA.img'

'r2_sub_13_av_cc_cc_HV.img'

'r2_sub_13_av_cc_cc_LV.img'

'r2_sub_13_av_cc_cc_zHA.img'

'r2_sub_13_av_cc_cc_zLA.img'

'r2_sub_14_av_cc_cc_HV.img'

'r2_sub_14_av_cc_cc_LV.img'

'r2_sub_14_av_cc_cc_zHA.img'

'r2_sub_14_av_cc_cc_zLA.img'

'r2_sub_15_av_cc_cc_HV.img'

'r2_sub_15_av_cc_cc_LV.img'

'r2_sub_15_av_cc_cc_zHA.img'

'r2_sub_15_av_cc_cc_zLA.img'

'r2_sub_16_av_cc_cc_HV.img'

'r2_sub_16_av_cc_cc_LV.img'

'r2_sub_16_av_cc_cc_zHA.img'

'r2_sub_16_av_cc_cc_zLA.img'

'r2_sub_17_av_cc_cc_HV.img'

'r2_sub_17_av_cc_cc_LV.img'

'r2_sub_17_av_cc_cc_zHA.img'

'r2_sub_17_av_cc_cc_zLA.img'

};

clear IN; clear F; clear I;

IN.N_subs = [12 17];

IN.Between = [1 2];  

IN.BetweenLabs = {{'All'} {'Group1', 'Group2'}};

IN.Within = [2 2];

IN.WithinLabs = {{'HV' 'LV' } {'HA' 'LA'}};

IN.FactorLabs = {'F1' 'F2' };

IN.Interactions = {[2 3] [2 4] [3 4] [2 3 4]};

IN.EqualVar = [1 0 1 1]; %or [1 0 0 0]

IN.Independent = [1 1 0 0];

F = CreateDesign2(IN);

figure(20); imagesc(F.XX); shg

I.OutputDir = pwd;

I.F = F;

I.Scans = Scans;

I.Mask = ['G:\mask.nii'];

I.RemoveOutliers = 1; % 0 !!

I.minN = 2;

I.DoOnlyAll = 0;

I.CompOpt=0;

I = GLM_Flex2(I);

I.Cons(1).name = 'Group by Arousal';

I.Cons(1). Groups = {12 13 14 15};

I.Cons(1).Levs = [2 2];

I.Cons(1).ET = [];

I.Cons(1).mean = 0;

I.Cons(2).name = 'Arousal Group1';

I.Cons(2). Groups = {12 13};

I.Cons(2).Levs = [2];

I.Cons(2).ET = [];

I.Cons(2).mean = 0;

I.Cons(3).name = 'Arousal Group2';

I.Cons(3). Groups = {14 15};

I.Cons(3).Levs = [2];

I.Cons(3).ET = [];

I.Cons(3).mean = 0;

I.Cons(4).name = 'Arousal Effect';

I.Cons(4).Groups = {6 7};

I.Cons(4).Levs = [2];

I.Cons(4).ET = [];

I.Cons(4).mean = 0;

I = GLM_Flex_Contrasts2(I);

% global FWHMxCondition;

% global FWHMyCondition;

% global FWHMzCondition;

Can someone help me understand why the mask is not used?

Thank you in advance

Haris

[Aaron Schultz]

To start this code is for the older version of GLM_Flex, not the newer
GLM_Flex_Fast. Please see here for you to setup and run analyses with
GLM_FLex_Fast2 or GLM_FLex_Fast4.

http://mrtools.mgh.harvard.edu/index.php?title=GLM_Flex_Fast2

-Aaron

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