AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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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