Bayes Factor Maps

In this example we use the estimateBayesFactor method, which converts statistic images to maps of (log) Bayes Factors. For now it works for t-maps, correlation maps, and maps of proportions (e.g., the number of subjects showing an effect). This walkthrough will show one example of all 3 of these types of maps.

The example uses the emotion regulation data provided with CANlab_Core_Tools. This dataset consists of a set of contrast images for 30 subjects from a first level analysis. The contrast is [reappraise neg vs. look neg], reappraisal of negative images vs. looking at matched negative images. These data were published in: Wager, T. D., Davidson, M. L., Hughes, B. L., Lindquist, M. A., Ochsner, K. N.. (2008). Prefrontal-subcortical pathways mediating successful emotion regulation. Neuron, 59, 1037-50.

Load Emotion Regulation data
Compute t-map for comparison of reappraise vs. look
Compute map of Bayes Factors based on t-statistic and sample size
Compute correlations between reappraise vs look and behavioral measure
Compute map of Bayes Factors based on pearson correlations and sample size
Compute proportion of subjects with greater activation during reappraisal
Compute map of Bayes Factors based on proportion and sample size

Load Emotion Regulation data

% load fmri object for reappraise vs look
image_obj=load_image_set('emotionreg');

% load text file with behavior
behav_data=importdata(which('Wager_2008_emotionreg_behavioral_data.txt'));

% store as single variable
reappraisal_success=behav_data.data(:,2);
image_obj.Y=reappraisal_success;

Loaded images:
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii
/home/lukie/CanlabCore/CanlabCore/Sample_datasets/Wager_et_al_2008_Neuron_EmotionReg/Wager_2008_emo_reg_vs_look_neg_contrast_images.nii

Compute t-map for comparison of reappraise vs. look

t=ttest(image_obj);
orthviews(t);

One-sample t-test
Calculating t-statistics and p-values

SPM12: spm_check_registration (v6245)              16:19:51 - 17/12/2018
========================================================================
Display <a href="matlab:spm_image('display','/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Warning: Function vecnorm has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.

Compute map of Bayes Factors based on t-statistic and sample size

% estimate BF
BF_tstat=estimateBayesFactor(t,'t');

% threshold from -6 to 6
BF_tstat_th = threshold(BF_tstat, [-6 6], 'raw-outside');

% show results
orthviews(BF_tstat_th);

Keeping vals outside of -6.000 to 6.000: 2174 voxels in .sig

SPM12: spm_check_registration (v6245)              16:20:21 - 17/12/2018
========================================================================
Display <a href="matlab:spm_image('display','/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Warning: Function vecnorm has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.

Compute correlations between reappraise vs look and behavioral measure

% initialize stats object from t-test output
r=t;

% replace data with simple correlation
r.dat=corr(image_obj.dat',image_obj.Y);

% show results
orthviews(r);

SPM12: spm_check_registration (v6245)              16:20:22 - 17/12/2018
========================================================================
Display <a href="matlab:spm_image('display','/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Warning: Function vecnorm has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.

Compute map of Bayes Factors based on pearson correlations and sample size

% estimate BF
BF_correlation=estimateBayesFactor(r,'r');

% threshold from -6 to 6
BF_correlation_th = threshold(BF_correlation, [-6 6], 'raw-outside');

% show results
orthviews(BF_correlation_th);

Keeping vals outside of -6.000 to 6.000: 273 voxels in .sig

SPM12: spm_check_registration (v6245)              16:20:49 - 17/12/2018
========================================================================
Display <a href="matlab:spm_image('display','/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Warning: Function vecnorm has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.

Compute proportion of subjects with greater activation during reappraisal

% initialize stats object from correlation output
prop=r;

% compute number of subjects with greater response in reappraisal
prop.dat=sum(image_obj.dat'>0)';

%show results
orthviews(prop);

SPM12: spm_check_registration (v6245)              16:20:50 - 17/12/2018
========================================================================
Display <a href="matlab:spm_image('display','/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Warning: Function vecnorm has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.

Compute map of Bayes Factors based on proportion and sample size

% estimate BF
BF_prop=estimateBayesFactor(prop,'prop');

% thresholhd from -6 to 6
BF_prop_th = threshold(BF_prop, [-6 6], 'raw-outside');

% show results
orthviews(BF_prop_th);

Keeping vals outside of -6.000 to 6.000: 2411 voxels in .sig

SPM12: spm_check_registration (v6245)              16:21:52 - 17/12/2018
========================================================================
Display <a href="matlab:spm_image('display','/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/home/lukie/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Warning: Function vecnorm has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.