3dMVM Output - Limit Voxels to White Matter

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1

I am using 3dMVM to analyze three groups. See the script below. How do I limit the voxels to white matter only in the output? See the output image below.

3dMVM -prefix Test5.nii -jobs 24
-bsVars SDS_deficit
-qVars “Age,Sex,RMS_rel_av”
-num_glt 3
-gltLabel 1 ‘nds-ds’ -gltCode 1 ‘SDS_deficit: +10 -11’
-gltLabel 2 ‘nds-hc’ -gltCode 2 ‘SDS_deficit: +10 -12’
-gltLabel 3 ‘ds-hc’ -gltCode 3 ‘SDS_deficit: +11 -12’
-mask IIT2.nii
-dataTable
Subj SDS_deficit Age Sex RMS_rel_av InputFile
sub-control01 2 28 2 0.0023 sub-control01.ses-01.FA.warped_5mm.resample.rotate.nii
sub-control02 2 23 1 0.0061 sub-control02.ses-01.FA.warped_5mm.resample.rotate.nii
sub-control03 2 25 1 0.0035 sub-control03.ses-01.FA.warped_5mm.resample.rotate.nii \ …

Test5.png
Test5.png976×422 317 KB

2

You can mask your data with a white matter mask created from a segmentation procedure - either one from FreeSurfer or using AFNI’s 3dSeg. The FreeSurfer white matter mask is in a few different places when it is processed with @SUMA_MakeSpecFS including the wm.seg.nii dataset. Apply the mask to your dataset with

3dcalc -a mydset -b wm.seg.nii -expr ‘a*step(b)’ -prefix mywmmasked.nii.gz

3

Thanks, Daniel. 3dcalc worked.