Hi, Osman-
Thanks for sending a copy of some of the APQC HTML. Attached is the critical part that I suggested looking at---the ve2a, which shows the EPI-anatomical alignment. Because your initial EPI and anatomical are a bit far apart (shown in the vorig block of the APQC), I suggest adding the option "-giant_move" to your afni_proc.py command in the '-align_opts_aea ..' part of controlling alignment of EPI and anatomical (= AEA), like this:
#!/bin/tcsh
afni_proc.py \
-subj_id FT.11b.rest \
-blocks despike tshift align tlrc volreg blur mask \
scale regress \
-copy_anat anat+orig \
-dsets func+orig.HEAD \
-tcat_remove_first_trs 2 \
-align_opts_aea -cost lpc+ZZ -giant_move \
-tlrc_base TT_N27+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_warp_dxyz 2.5 \
-blur_size 4 \
-mask_segment_anat yes \
-mask_segment_erode yes \
-mask_import Tvent template_ventricle_2.5mm+tlrc \
-mask_intersect Svent CSFe Tvent \
-mask_epi_anat yes \
-regress_motion_per_run \
-regress_ROI_PC Svent 3 \
-regress_ROI_PC_per_run Svent \
-regress_make_corr_vols WMe Svent \
-regress_anaticor_fast \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.05 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim yes
Also, I don't see the motion plots in your QC. I was a bit surprised by that. What is the output of:
afni_system_check.py -check_all
?
--pt
Attachments:
open |
download -
img_part_of_apqc_ve2a.png
(453 KB)