3dMVM

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1

Hi AFNI Experts,

I am running 3dMVM to model a Group (2 levels) by Emotion Task (3 levels) interaction. I am using an amygdala mask to restrict the analyses to amygdala voxels. I have successfully done this analysis using a cingulate mask.

However, when I get to the amygdala mask, it says that the model is failing. The script is exactly the same, except the mask is different.

Could it be failing because the mask is to small? The sample sizes are quite small with 15 in one group and 13 in another.

Thanks,

Emily

Below is my script:

#!/bin/tcsh

cd /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images

3dMVM -prefix Frontal_ANOVA -jobs 4
-bsVars Group
-wsVars ‘Emotion’
-SC
-mask /Users/emilybelleau/Documents/Group_Analyses_MID/ROIs-2/amg_resampled.nii
-dataTable
Subj Group Emotion InputFile
Sub1 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject1.nii
Sub1 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject1.nii
Sub1 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject1.nii
Sub2 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject2.nii
Sub2 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject2.nii
Sub2 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject2.nii
Sub13 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject13.nii
Sub13 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject13.nii
Sub13 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject13.nii
Sub15 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject15.nii
Sub15 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject15.nii
Sub15 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject15.nii
Sub21 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject15.nii
Sub21 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject15.nii
Sub21 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject15.nii
Sub22 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject22.nii
Sub22 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject22.nii
Sub22 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject22.nii
Sub24 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject24.nii
Sub24 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject24.nii
Sub24 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject24.nii
Sub25 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject25.nii
Sub25 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject25.nii
Sub25 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject25.nii
Sub26 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject26.nii
Sub26 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject26.nii
Sub26 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject26.nii
Sub27 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject27.nii
Sub27 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject27.nii
Sub27 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject27.nii
Sub29 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject29.nii
Sub29 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject29.nii
Sub29 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject29.nii
Sub30 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject30.nii
Sub30 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject30.nii
Sub30 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject30.nii
Sub31 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject31.nii
Sub31 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject31.nii
Sub31 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject31.nii
Sub4 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject4.nii
Sub4 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject4.nii
Sub4 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject4.nii
Sub8 BPD Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject8.nii
Sub8 BPD Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject8.nii
Sub8 BPD Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject8.nii
Sub10 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject10.nii
Sub10 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject10.nii
Sub10 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject10.nii
Sub12 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject12.nii
Sub12 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject12.nii
Sub12 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject12.nii
Sub14 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject14.nii
Sub14 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject14.nii
Sub14 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject14.nii
Sub16 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject16.nii
Sub16 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject16.nii
Sub16 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject16.nii
Sub17 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject17.nii
Sub17 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject17.nii
Sub17 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject17.nii
Sub19 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject19.nii
Sub19 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject19.nii
Sub19 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject19.nii
Sub20 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject20.nii
Sub20 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject20.nii
Sub20 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject20.nii
Sub23 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject23.nii
Sub23 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject23.nii
Sub23 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject23.nii
Sub3 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject3.nii
Sub3 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject3.nii
Sub3 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject3.nii
Sub5 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject5.nii
Sub5 Bip Fear //Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject5.nii
Sub5 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject5.nii
Sub6 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject6.nii
Sub6 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject6.nii
Sub6 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject6.nii
Sub7 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject7.nii
Sub7 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject7.nii
Sub7 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject7.nii
Sub9 Bip Angry /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/AngryNeutral/con_0003_Subject9.nii
Sub9 Bip Fear /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/FearNeutral/con_0002_Subject9.nii
Sub9 Bip Happy /Users/emilybelleau/Documents/Group_Analyses_MID/contrast_images/HappyNeutral/con_0001_Subject9.nii

2

Could it be failing because the mask is to small?

Yes, that is exactly what happened in this case. You don’t have to rerun the analysis with the mask; instead you just apply the mask to the output from the previous analysis without the mask.

3

Hi Gang,

Thanks so much! I am a bit confused…how would I apply the mask to the output of 3dMVM? So I have my lets say whole brain ANOVA with my main effects and interaction. Is there a way to then restrict my analyses to the mask (for small volume correction…use amygdala as a search space) in the gui? Or are you saying to just extract the parameter estimates from the entire amygdala mask? I was initially planning to use the mask as a search space. Are there any significant voxels within this mask, not necessarily the entire mask.

Thank you,

Emily

4

Is there a way to then restrict my analyses to the mask (for small volume correction…use amygdala as a search space) in the gui?

For visualization, you can do this:

3dcalc -a 3dLMEresults -b yourMask -expr ‘a*b’ -prefix maskedResults

For FWE correction, use option -mask in 3dClustSim.