library(ANTsR)
 system("3dcalc -expr a -a '/software/AFNI_25.2.06/MNI152_2009_template_SSW.nii.gz[0]' -prefix MNI152_2009_template.nii.gz")
 system("3dcalc -expr a -a '/software/AFNI_25.2.06/MNI152_2009_template_SSW.nii.gz[3]' -prefix MNI152_2009_mask.nii.gz")
temp=antsImageRead('MNI152_2009_template.nii.gz')
mask=antsImageRead('MNI152_2009_mask.nii.gz',pixeltype= 'unsigned int')
km=kmeansSegmentation(temp,3,mask)
antsImageWrite(km$probabilityimages[[1]],'MNI152_2009_CSF.nii.gz')
 system("3dcalc -a MNI152_2009_CSF.nii.gz -expr 'step(a-.9)' -prefix MNI152_2009_CSF_bi.nii.gz")
 system("3dclust -NN3 6000 -savemask MNI152_2009_CSF_mask.nii.gz MNI152_2009_CSF_bi.nii.gz")
 system("3dcalc -a ./MNI152_2009_CSF_mask.nii.gz -expr 'step(a-1)' -prefix MNI152_2009_Vent.nii.gz")
 system('3drefit -view tlrc -space MNI MNI152_2009_Vent.nii.gz')
 system('3dresample -dxyz 4 4 4 -inset MNI152_2009_Vent.nii.gz -prefix template_ventricle_4mm.nii.gz')
 system('3drefit -view tlrc -space MNI template_ventricle_4mm.nii.gz')