Good morning AFNI gurus - couple questions for you. I am trying to use freesurfer grey matter for my anatomical dataset for preprocessing.
afni_proc.py command is:
afni_proc.py -subj_id $name \
-script proc.$name -scr_overwrite \
-dsets $name/$name.rest1+orig.HEAD $name/$name.rest2+orig.HEAD\
-copy_anat /Volumes/Faraday/DATA/ELS_Pilot/$name/$name.freesurfer/mri/SUMA/aparc+aseg.nii \
-blocks despike tshift align tlrc volreg mask scale regress \
-tcat_remove_first_trs 4 \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_segment_anat yes \
-regress_censor_motion 1.5 \
-regress_censor_outliers 0.5 \
-regress_bandpass 0.009 0.08 \
-regress_apply_mot_types demean deriv \
-regress_run_clustsim no \
-regress_est_blur_errts \
-out_dir $name/$name.proc_rsfc \
-remove_preproc_files \
-execute
end
exit
Two questions, first the operational: I am having some trouble using freesurfer processed anatomicals in afni_proc.py. It looks like AFNI is getting stuck trying to skullstrip. the error is:
Fatal Signal 11 (SIGSEGV) received
SUMA_SurfGridIntersect
SUMA_FindVoxelsInSurface
3dSkullStrip
Bottom of Debug Stack
** AFNI version = AFNI_2011_12_21_1014 Compile date = May 23 2014
** [[Precompiled binary macosx_10.7_Intel_64: May 23 2014]]
** Program Abort **
....
** ERROR: Could not strip skull
** ERROR - script failed
@auto_tlrc -base TT_N27+tlrc -input aparc+aseg_ns+orig -no_ss
Error: Anatomical dset aparc+aseg_ns+orig not found.
Second - more theoretical question - would using a freesurfer-based grey matter map affect with outlier detection? I have traditionally been using tissue-based maps for this (different proc script).
Any thoughts, assistance, input is appreciated!
Noah
