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  

|
JW
November 16, 2020 09:29PM
Dear AFNI experts,

Hope you all are staying safe. I downloaded unprocessed resting-state data from the Human Connectome project where they had 4 scans for each participant (Session 1 L to R, Session 1 R to L, Session 2 L to R, Session 2 R to L). These 4 epi data were concatenated using 3dTcat and submitted to the proc py script like below.

afni_proc.py \
-blocks despike align tlrc volreg blur mask regress \
-copy_anat /Volumes/LAVA/"$subj"/anat/"$subj"_anat+orig \
-anat_follower_ROI aaseg anat /Volumes/LAVA/"$subj"/anat/aparc.a2009s+aseg.nii \
-anat_follower_ROI aeseg epi /Volumes/LAVA/"$subj"/anat/aparc.a2009s+aseg.nii \
-anat_follower_ROI FSvent epi /Volumes/LAVA/"$subj"/anat/"$subj"_vent.nii \
-anat_follower_ROI FSWm epi /Volumes/LAVA/"$subj"/anat/"$subj"_wm.nii \
-anat_follower_erode FSvent FSWm \
-dsets /Volumes/LAVA/"$subj"/trunc_rest_"$subj"+orig \
-out_dir Proc_results \
-script py_result_"$subj"_script \
-scr_overwrite \
-subj_id "$subj" \
-align_opts_aea -cost lpc+ZZ -giant_move \
-tlrc_base MNI152_T1_2009c+tlrc \
-tlrc_NL_warp \
-tlrc_NL_awpy_rm no \
-tlrc_no_ss \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_warp_dxyz 2.0 \
-regress_apply_mask \
-regress_ROI_PC FSvent 3 \
-regress_make_corr_vols aeseg FSvent \
-regress_anaticor_fast \
-regress_anaticor_label FSWm \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts

tcsh -xef py_result_"$subj"_script |& tee output.py_result_"$subj"_script

@ linenum++
end


In the middle of the proc py, I just had an error that I have never seen before (below).

** FATAL ERROR: -polort value can't be over 20 sad smiley

Could you please let me know what caused this issue and how to solve this?

Best,
JW
Subject Author Posted

resting state proc py error

JW November 16, 2020 09:29PM

Re: resting state proc py error

ptaylor November 17, 2020 10:37PM

Re: resting state proc py error

JW November 18, 2020 09:10AM

Re: resting state proc py error

rick reynolds November 19, 2020 11:27AM

Re: resting state proc py error

JW November 19, 2020 02:35PM

Re: resting state proc py error

rick reynolds November 19, 2020 02:48PM

Re: resting state proc py error

JW November 19, 2020 03:21PM

Re: resting state proc py error

gang November 19, 2020 08:45PM

Re: resting state proc py error

JW November 20, 2020 08:31AM

Re: resting state proc py error

gang November 20, 2020 10:53AM

Re: resting state proc py error

gang November 20, 2020 06:27PM

Re: resting state proc py error

JW November 23, 2020 12:38PM

Re: resting state proc py error

gang November 24, 2020 10:32AM