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

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Robin
October 25, 2016 09:57AM
Let me revive this!

We want to use ANATICOR in our task based data analysis but I don't see how it helps me? I realized that the ANATICOR part is run after 3dDeconvole (I guess that is what Rick mean with 3dREML.fit). So how is this helping me, the ANATICOR info is not in the big regression? I want my stats output to be cleaned from the noise that ANATICOR takes care of (spatially varying WM noise). But only the residuals are "cleaned" with ANATICOR? How do I use this?

Or do I misunderstand what 3dREML.fit does? 

afni_proc.py -subj_id $sub_id \
    -dsets $fmri_data \
    -copy_anat $T1_data \
    -blocks despike tshift align volreg mask regress \
    -mask_segment_anat yes \
    -mask_segment_erode yes \
    -align_opts_aea \
	-giant_move \
    -tcat_remove_first_trs 0 \
    -volreg_align_to MIN_OUTLIER \
    -volreg_align_e2a \
    -regress_censor_motion 0.3 \
    -regress_censor_outliers 0.1 \
    -regress_anaticor \
    -regress_reml_exec \
    -regress_apply_mot_types demean deriv \
    -regress_stim_types AM1 \
    -regress_basis 'dmBLOCK' \
    -regress_stim_times $stim/* \
    -regress_stim_labels Q_other Q_self C_other C_self O_other_dwn O_other_up O_self_dwn O_self_up motor \
    -regress_local_times \
        -regress_opts_3dD \
	-allzero_OK \
	-GOFORIT 6 \


Thanks!



Edited 3 time(s). Last edit at 10/25/2016 10:58AM by Robin.
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Subject Author Posted

ANATICOR with task data

Sara September 25, 2015 10:58PM

Re: ANATICOR with task data

rick reynolds September 27, 2015 08:59PM

Re: ANATICOR with task data

Robin October 25, 2016 09:57AM

Re: ANATICOR with task data

rick reynolds October 26, 2016 10:51AM

Re: ANATICOR with task data

Robin October 26, 2016 10:59AM

Re: ANATICOR with task data

rick reynolds October 26, 2016 12:08PM

Re: ANATICOR with task data

Bob Cox October 26, 2016 12:13PM

Re: ANATICOR with task data

Robin May 11, 2017 07:41AM

Re: ANATICOR with task data

rick reynolds May 11, 2017 07:57AM

Re: ANATICOR with task data

rick reynolds May 31, 2017 08:46AM