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November 30, 2020 02:43PM
Hello pt,

The results of the QC has been sent.

Here is the command:

@animal_warper -input dset_anat_deob -base studytemplatebrain -atlas Brain_label.nii \
-outdir ouput_dir_a_id -ok_to_exist -align_centers_meth OFF -cost nmi -skullstrip mask_brain.nii.gz -subj_id a_id -script ouput_dir_a_id + /proc. + a_id -scr_overwrite -out_dir ouput_dir_a_id + / + a_id + .results \
-blocks despike tshift align tlrc volreg blurmask regress \
-dsets dset_bold_deob_RECEN \
-copy_anat dset_anat_deob_RECEN \ 
-anat_has_skull no \
-tcat_remove_first_trs 5 -blip_reverse_dset dset_bold_deob_RECEN_inv \
-align_opts_aea -epi_strip 3dAutomask -cost nmi -giant_move -check_flip \
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -mask_epi_anat yes \       
-tlrc_base studytemplatebrain \
-tlrc_NL_warp -tlrc_NL_warped_dsets ouput_dir_a_id1 + /anatT1_deob_warp2std_nsu.nii.gz \
ouput_dir_a_id1 + /anatT1_deob_shft_al2std_mat.aff12.1D ouput_dir_a_id1 + /anatT1_deob_shft_WARP.nii.gz \ 
-regress_censor_motion 2 -regress_censor_outliers 0.05 -regress_motion_per_run \
-regress_apply_mot_types demean deriv -blur_size 2 -regress_run_clustsim \
 no -regress_est_blur_errts -html_review_style pythonic -execute \

note that:
the functional and the anat were centered prior to these 2 commands
the other sequences didn't have -blip_reverse_dset
and lpc+zz was also used depending on the result of the co-registration (sometimes it just didn't work with lpc+zz and sometimes didn't work with nmi...)

the templates was:
and I am currently trying:

thank you!
Subject Author Posted

Quality check with AFNI

Doughboys November 30, 2020 11:38AM

Re: Quality check with AFNI

ptaylor November 30, 2020 01:21PM

Re: Quality check with AFNI

Doughboys November 30, 2020 02:43PM

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