3dttest++ results

[LuisaBoh]

Hello AFNI

I ran 3dttest++ to compare the CBF values of 2 groups. I used the -mask flag which is supposed that restrict my analysis to the mask I am using (just gray matter excluding cerebellum) and I am having results that are showing me some white matter voxels, what am I doing wrong? Here is my 3dttest code

3dttest++ -mask GMmask__MNI152_2009_noCerebellum_final.nii
-prefix GriefvsHC_AFNI_Mask_CovariateswGM_DIFF_noCerebellum
-prefix_clustsim GriefvsHC_AFNI_Mask_CovariateswGM_DIFF_noCerebellum
-tempdir /scratch/global/lbohorquez/Brianna/results/Luisa/temp
-covariates Covariates_wGM.txt"[0,1,2,3]"
-center DIFF
-Clustsim 24
-toz
-setA Grief
172 ASL_CBF_2MNI_6mm_172_120916.nii \
…more subjects…
-setB HC
198 ASL_CBF_2MNI_6mm_198_061814.nii
…more subjects…

[ptaylor]

Hi-

I am not familiar with this dataset inherently:
GMmask__MNI152_2009_noCerebellum_final.nii

Could you please try overlaying that on the MNI162_2009, and verify that it covers the restricted portion of the brain that you expect?

(You could also underlay that mask with your GriefvsHC_AFNI_Mask_CovariateswGM_DIFF_noCerebellum* results, and verify that they are within the mask.

–pt