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August 10, 2018 03:13PM
Hi, upon reviewing the output script generated by afni_proc.py, I noticed that the options for 3dBlurInMask were not what I expected. I'm trying to blur only in the gray matter eroded mask with a fwhm of 5.0 mm. The following is the afni_proc.py script:

afni_proc.py -subj_id $subj \
-script proc.SS.$subj -scr_overwrite \
-blocks despike align tlrc volreg mask blur scale regress \
-copy_anat $top_dir/SSWarper_Output/anatSS.test_sub.nii \
-anat_has_skull no \
-dsets $epi \
-tcat_remove_first_trs $trs \
-align_opts_aea -giant_move -cost lpc+zz \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-tlrc_base MNI152_T1_2009c+tlrc \
-volreg_warp_dxyz 2.0 \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
../../../SSWarper_Output/anatQQ.test_sub.nii \
../../../SSWarper_Output/anatQQ.test_sub.aff12.1D \
../../../SSWarper_Output/anatQQ.test_sub_WARP.nii \
-blur_in_mask yes \
-blur_opts_BIM \
-mask GMe \
-FWHM 5.0 \
-mask_segment_anat yes \
-mask_segment_erode yes \
-regress_motion_per_run \
-regress_bandpass 0.01 0.25 \
-regress_RSFC \
-regress_ROI WMe brain CSFe \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_run_clustsim no

The output script, however, contains these blurring options:

# ================================== blur ==================================
# blur each volume of each run
foreach run ( $runs )
3dBlurInMask -preserve -FWHM 4.0 -Mmask full_mask.$subj+tlrc \
-prefix pb03.$subj.r$run.blur \
pb02.$subj.r$run.volreg+tlrc
end

Am I using blur_opts_BIM incorrectly?
Subject Author Posted

Usage of blur_opts_BIM

Daniel Zhu August 10, 2018 03:13PM

Re: Usage of blur_opts_BIM

rick reynolds August 13, 2018 04:31PM

Re: Usage of blur_opts_BIM

Daniel Zhu August 14, 2018 08:11PM



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