Hello,

I am using uber_subject.py to create my preprocessing steps. I have not changed much from the default settings. However, I am having an issue with skull stripping, which is performed via align_epi_anat.py. My MPRage images are collected in the sagittal orientation, which may be creating the problem?? When I look at my skull_stripped image, there are errors with it -see the attachment specifically in the sagittal view. Do you have any suggestions?

Below is the code from the processing script from uber_subject.py

# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, t1mpragesagp2isos002a1001_ns+orig)
align_epi_anat.py -anat2epi -anat t1mpragesagp2isos002a1001+orig \
-save_skullstrip -suffix _al_junk \
-epi min_outlier_volume+orig -epi_base 0 \
-epi_strip 3dAutomask \
-volreg off -tshift off

# ================================== tlrc ==================================
# warp anatomy to standard space
@auto_tlrc -base TT_N27+tlrc -input t1mpragesagp2isos002a1001_ns+orig -no_ss

# store forward transformation matrix in a text file
cat_matvec t1mpragesagp2isos002a1001_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D