Hi!
Whoops, I did mean to copy-paste the command... It's:
afni_proc.py \
-blocks despike tshift align tlrc volreg mask combine blur scale regress \
-copy_anat t1.nii \
-anat_has_skull yes \
-dsets_me_echo f_e1*.nii \
-dsets_me_echo f_e2*.nii \
-dsets_me_echo f_e3*.nii \
-echo_times 12.0 28.0 44.0 \
-reg_echo 2 \
-tcat_remove_first_trs 10 \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
-tlrc_base MNI152_T1_2009c+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a -volreg_tlrc_warp \
-mask_epi_anat yes \
-mask_segment_anat yes \
-mask_segment_erode yes \
-combine_method tedana \
-combine_tedana_path /software/system/tedana/20200226/bin/tedana \
-blur_size 6 \
-blur_in_mask yes \
-regress_bandpass 0.01 0.08 \
-regress_ROI WMe CSF \
-regress_motion_per_run \
-regress_censor_motion 3.0 \
-regress_censor_outliers 0.05 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-html_review_style pythonic
And I also make a few changes, namely:
1) 3dTshift - Remove '-tzero 0' and add '-TR 2.5s -tpattern seqminus' instead;
2) combine:
a) remove the following:
tedana_wrapper.py -input pb02.$subj.r$run.e*.tshift+orig.BRIK \
-TE $echo_times \
-mask mask_epi_anat.$subj+orig \
-results_dir tedana_r$run \
-ted_label r$run \
-tedana_prog /software/system/tedana/20200226/bin/tedana \
-prefix tedprep
and add instead this:
tedana -d pb03.SUBJ.r01.e01.volreg+tlrc.BRIK \
pb03.SUBJ.r01.e02.volreg+tlrc.BRIK \
pb03.SUBJ.r01.e03.volreg+tlrc.BRIK \
-e 12.0 28.0 44.0 --mask mask_epi_anat.SUBJ+tlrc.BRIK --debug
b) Change '3dcopy tedana_r$run/TED.r$run/dn_ts_OC.nii pb03.$subj.r$run.combine' to '3dcopy dn_ts_OC.nii pb04.$subj.r$run.combine+orig'
By the way, I've also tried with and without giant move but nothing changes really.
I've attached the output for 've2a'. For some reason, I don't have the vorig block, but I've attached the raw T1 and EPI images (raw.png) - the panels are showing raw EPI, anat overlaid on EPI and then 3 panels where the EPI is overlaid on the anat (EPI is colourful in panels 2-5).
Cheers!
Misho
Edited 1 time(s). Last edit at 05/11/2021 02:00PM by ptaylor.
