LABELS in afni_proc.py

AFNI Message Board
1

Hi,

Quick question about LABELs in afni_proc.py. If I pass the following arguments to afni_proc.py


-anat_follower_ROI aaseg  anat ${SumaDir}/aparc.a2009s+aseg.nii        \
             -anat_follower_ROI aeseg  epi  ${SumaDir}/aparc.a2009s+aseg.nii        \
             -anat_follower_ROI FSvent epi ${subject}_vent.nii                  \
             -anat_follower_ROI FSW    epi ${subject}_WM.nii                   \
             -anat_follower_erode FSvent FSW                           \

In a subsequent -regress_ROI argument, how do I refer to the eroded datasets by label name? Do I just tack an ‘e’ on the the labels supplied to -anat_follower_erode? So, in this case, FSvente and FSWe?

Thanks,

Colm.

2

Hi, Colm-

I think it would just be using that same label:


-regress_ROI FSWe                                        \

There is a closely related example of this in afni_proc.py for one of Gang’s papers here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/codex/main_det_2016_ChenEtal.html
… which demonstrates some similar use


# Input data: FreeSurfer results (anatomy, ventricle and WM maps)
set fsanat = ${subj}_SurfVol.nii
set fsvent = FSmask_vent.nii
set fswm   = FSmask_WM.nii

afni_proc.py -subj_id $subj.$task                                       \
    -blocks despike tshift align tlrc volreg blur mask regress          \
    -copy_anat $fsindir/$fsanat                                         \
    -anat_follower_ROI aaseg  anat $fsindir/aparc.a2009s+aseg_rank.nii  \
    -anat_follower_ROI aeseg  epi  $fsindir/aparc.a2009s+aseg_rank.nii  \
    -anat_follower_ROI FSvent epi  $fsindir/$fsvent                     \
    -anat_follower_ROI FSWMe  epi  $fsindir/$fswm                       \
    -anat_follower_erode FSvent FSWMe                                   \
    -dsets $epi_dpattern                                                \
    -tcat_remove_first_trs 0                                            \
    -tlrc_base TT_N27+tlrc                                              \
    -tlrc_NL_warp                                                       \
    -volreg_align_to MIN_OUTLIER                                        \
    -volreg_align_e2a                                                   \
    -volreg_tlrc_warp                                                   \
    -regress_ROI_PC FSvent 3                                            \
    -regress_make_corr_vols aeseg FSvent                                \
    -regress_anaticor_fast                                              \
    -regress_anaticor_label FSWMe                                       \
    -regress_censor_motion 0.2                                          \
    -regress_censor_outliers 0.1                                        \
    -regress_apply_mot_types demean deriv                               \
    -regress_est_blur_epits                                             \
    -regress_est_blur_errts                                             \
    -regress_run_clustsim no

–pt