You mean you want to remove everything but the WM labels? You can do it in two steps:

1. Create a mask of the wm labels:

mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o wm.mask.nii.gz

2. Mask the wmparc:

mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz

Hi Freesurfer experts,

I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM.

I used the following command for growing the parcellation into WM:

mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz

Would appreciate help and suggestions!

Thanks,

Michiko.

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