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May 11, 2021 08:17AM
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.


Subject Author Posted

(Mis)alignment Attachments

misho_dimitrov May 10, 2021 12:07PM

Re: (Mis)alignment

ptaylor May 10, 2021 12:53PM

Re: (Mis)alignment Attachments

misho_dimitrov May 11, 2021 08:17AM

Re: (Mis)alignment Attachments

ptaylor May 11, 2021 02:19PM

Re: (Mis)alignment

ptaylor May 11, 2021 02:45PM

Re: (Mis)alignment

misho_dimitrov May 20, 2021 05:33AM

Re: (Mis)alignment

ptaylor June 09, 2021 05:06PM



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