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  

Previous Message Next Message
Message List New Topic Print View
|
Philipp
May 09, 2022 02:17PM
Thanks for the explanation.

When adding 
-regress_compute_fitts \

to my AFNI proc script, it fails with the following message. 

** cannot compute fitts, have 3dD_stop but no reml_exec
** script creation failure for block 'regress'

Any clue what is wrong here? Is something in my script wrong? 

...
afni_proc.py \
-subj_id ${subject}_Run \
-out_dir $directory_run/Results \
-dsets \
	$directory_deoblique/Run_deoblique+orig \
-blocks despike tshift align tlrc volreg mask blur regress \
-copy_anat $directory_sswarper/anatSS.$subject.nii \
-anat_has_skull no \
-tcat_remove_first_trs 4 \
-align_opts_aea -cost lpc+ZZ \
-volreg_align_e2a \
-volreg_align_to MIN_OUTLIER \
-volreg_tlrc_warp -tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
	$directory_sswarper/anatQQ.$subject.nii \
	$directory_sswarper/anatQQ.$subject.aff12.1D \
	$directory_sswarper/anatQQ.${subject}_WARP.nii \
-volreg_post_vr_allin yes \
-volreg_pvra_base_index MIN_OUTLIER \
-mask_segment_anat yes \
-mask_segment_erode yes \
-regress_compute_fitts \
-regress_polort 2 \
-regress_bandpass 0.01 1 \
-regress_anaticor \
-regress_ROI WMe CSFe \
-regress_apply_mot_types demean deriv \
-regress_motion_per_run \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-blur_size 8.0 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-html_review_style pythonic \
-execute

Update: ok, I see that I had to add 
-regress_reml_exec \
when using 
-regress_compute_fitts

Another update:
The processing step 
++ detrending starts: 153 baseline funs; 2268 time points
is now finally done after around an hour for one subject. Before, even after two or three hours, this step was still not done (when using the standard 34 polorts).
Therefore, it appears that AFNI is much faster using 
-regress_polort 2         \
-regress_bandpass 0.01 1

Thanks Rick!



Edited 4 time(s). Last edit at 05/09/2022 02:37PM by Philipp.
Reply Quote
RSS
Subject Author Posted

AFNI proc -regress_polort option for very long runs

Philipp May 07, 2022 08:47AM

Re: AFNI proc -regress_polort option for very long runs

rick reynolds May 09, 2022 11:55AM

Re: AFNI proc -regress_polort option for very long runs

Philipp May 09, 2022 12:32PM

Re: AFNI proc -regress_polort option for very long runs

rick reynolds May 09, 2022 02:08PM

Re: AFNI proc -regress_polort option for very long runs

Philipp May 09, 2022 02:17PM

Re: AFNI proc -regress_polort option for very long runs

rick reynolds May 09, 2022 02:39PM

Re: AFNI proc -regress_polort option for very long runs

Philipp May 09, 2022 02:44PM

Re: AFNI proc -regress_polort option for very long runs

rick reynolds May 09, 2022 02:51PM

Re: AFNI proc -regress_polort option for very long runs

Philipp May 09, 2022 02:58PM

Re: AFNI proc -regress_polort option for very long runs

rick reynolds May 09, 2022 03:31PM

Re: AFNI proc -regress_polort option for very long runs

Philipp May 09, 2022 03:35PM

Re: AFNI proc -regress_polort option for very long runs

rick reynolds May 09, 2022 04:10PM