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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September 04, 2020 08:20AM
Hi!

I have a subject with quite a lot of censoring. However, the following afni_proc works well:

afni_proc.py -subj_id sub11 -script proc.sub11 -scr_overwrite -blocks \
despike tshift align tlrc volreg blur mask regress -copy_anat \
/anatomy/sub11.nii -dsets \
/resting_state/sub11_1.nii \
/resting_state/sub11_2.nii \
-tcat_remove_first_trs 0 -align_opts_aea -giant_move -volreg_align_to \
MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -blur_size 4.0 \
-regress_censor_motion 0.25 -regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv -regress_motion_per_run \
-regress_est_blur_errts -regress_run_clustsim no


Now, I'm trying to understand why it crashes when I try a similar thing, but also regressing out signal from white matter and vent. I get the message of: ** ERROR: total number of fixed regressors (250) is too many for 249 retained time points!
Is there a way to save this subject regressing out wm and ventricles? Here is the afni_proc code that leads to the error:

afni_proc.py -subj_id sub11 -script proc.sub11 -scr_overwrite -blocks despike \
tshift align tlrc volreg blur mask regress -copy_anat \
/SUMA/sub11/T1.nii.gz -dsets \
/resting_state/sub11_1.nii \
/resting_state/sub11_2.nii \
-anat_follower_ROI aaseg anat \
/SUMA/sub11/aparc.a2009s+aseg.nii.gz \
-anat_follower_ROI aeseg epi \
/SUMA/sub11/aparc.a2009s+aseg.nii.gz \
-anat_follower_ROI FSvent epi \
/SUMA/sub11/fs_ap_latvent.nii.gz \
-anat_follower_ROI FSWe epi \
/SUMA/sub11/fs_ap_wm.nii.gz \
-anat_follower_erode FSvent FSWe -tcat_remove_first_trs 0 \
-align_opts_aea -giant_move -volreg_align_to MIN_OUTLIER \
-volreg_align_e2a -volreg_tlrc_warp -blur_size 4.0 \
-regress_censor_motion 0.25 -regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv -regress_motion_per_run \
-regress_est_blur_errts -regress_run_clustsim no -regress_ROI_PC FSvent \
3 -regress_ROI_PC_per_run FSvent -regress_make_corr_vols aeseg FSvent \
-regress_anaticor_fast -regress_anaticor_label FSWe


I appreciate any input. Thanks!
Subject Author Posted

censoring

Ana Navarro Cebrian September 04, 2020 08:20AM

Re: censoring

Cesar Caballero Gaudes September 06, 2020 03:30AM

Re: censoring

Ana Navarro Cebrian September 08, 2020 11:14AM