Hello,
I am currently using afni_proc.py to complete my pre-processing, and as I was completing my quality checks, I noticed that chunks of two participant's brains were removed during skull stripping. I used the various options indicated in 3dSkullStrip to help alleviate this problem but this did not help. Are there any other suggestions I can try? I have attached a copy of the resulting anatomical for both of these participants.
Various codes I used to fix the issue:
3dSkullStrip -input 11987.anat+orig -prefix 11987_skullstrip_1 -push_to_edge
3dSkullStrip -input 11987.anat+orig -prefix 11987_skullstrip_2 -ld 30
3dSkullStrip -input 11987.anat+orig -prefix 11987_skullstrip_4 -no_avoid_eyes
3dSkullStrip -input 11987.anat+orig -prefix 11987_skullstrip_5 -shrink_fac 0.5
3dSkullStrip -input 11987.anat+orig -prefix 11987_skullstrip_8 -blur_fwhm 2 -use_skull
3dSkullStrip -input 11987.anat+orig -prefix 11987_skullstrip_9 -blur_fwhm 2 -use_skull -avoid_vent -avoid_vent -init_radius 75
Thank you in advance for your help.
Best,
Tamara
