new afni_proc.py options

AFNI Message Board
1

Hello!
A few months ago I had been using afni_proc.py successfully with the following options (see below). I tried running new subjects through this script this week and have noticed that -anat_follower_ROI is no longer a viable option. Do you have any suggestions for what to use instead to ensure consistency with the outputs of previous scans processed with this script?:

afni_proc.py -subj_id ${SUBJID[$n]}${MRQID[$n]}
-out_dir $afnidir/${SUBJID[$n]}/${MRQID[$n]}/output
-script $afnidir/${SUBJID[$n]}/${MRQID[$n]}/proc_script.sh
-blocks regress
-copy_anat $fsdir/mri/aseg+orig
-anat_follower_ROI aaseg anat $fsdir/SUMA/aparc.a2009s+aseg_rank.nii
-anat_follower_ROI aeseg epi $fsdir/SUMA/aparc.a2009s+aseg_rank.nii
-anat_follower_ROI FSvent epi $fsdir/SUMA/${SUBJID[$n]}${MRQID[$n]}vent.nii
-anat_follower_ROI FSWe epi $fsdir/SUMA/${SUBJID[$n]}${MRQID[$n]}_WM.nii
-anat_follower_erode FSWe FSvent
-dsets $afnidir/${SUBJID[$n]}/${MRQID[$n]}/rRest_psn+orig
-regress_anaticor
-regress_anaticor_label FSWe
-regress_anaticor_radius ${WM}
-regress_motion_file $afnidir/${SUBJID[$n]}/${MRQID[$n]}/Rest_mt.1D
-regress_bandpass 0.01 0.1
-regress_ROI_PC FSvent 3
tcsh -xef $afnidir/${SUBJID[$n]}/${MRQID[$n]}/proc_script.sh 2>&1 | tee output.$afnidir/${SUBJID[$n]}/${MRQID[$n]}/proc_script.sh

Thanks,
Kate

2

Hi Kate,

That option should still work. What error are you seeing?

Note that the examples no longer use the rank datasets.

  • rick
3

** error: option -dsets follows unknown arg #11 (-anat_follower_ROI)

I thought this was odd so looked in the afni_proc.py -help output. There is nothing there to indicate -anat_follower_ROI is a valid option (I had been previously using example 11 as a template, but that seems to be gone as well.

4

Perhaps you are using an older version now?

afni -ver
afni_proc.py -ver

  • rick
5

afni -ver
Precompiled binary linux_openmp_64: Feb 19 2015 (Version AFNI_2011_12_21_1014)

afni_proc.py -ver
version 4.30, February 13, 2015

Would this version not have the current options?

6

The -anat_follower_ROI option is from May, 2015.

It might be worth updating that system anyway,
since the binaries are almost 2 years old.

  • rick
7

Thanks for the help, Rick!