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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March 30, 2021 01:38PM
Hello afni experts,

I have posted this question before
I am using afni_proc.py with the 3dREMLfit option for nuissance regression in resting state. I would like to get as additional output how much variance was removed by the noise model (including the motion regressors, tissue based regressors, drift etc).
The purpose is to evaluate how much variance was removed for each subjects depending on the no. of nuisance regressors I use.

How can I do this is afni_proc.py?

I tried using -rout but it does not output the R^2 stats for the error in resting state but only in task based analysis.
I am using the following script:

afni_proc.py -subj_id ${subj}\
-script proc.py_scripts_remltest/proc_${subj}.sh\
-out_dir ${top_dir}${subj}/${subj}.3dDeconvolve_remltest\
-dsets ${func_dir}pb04.P1002.scale_masked_Despiked_wds.nii.gz\
-blocks regress -regress_reml_exec -regress_opts_reml -rout -regress_motion_file /tmp/mri2/hierarchical/BOLD_variability/data/P1/G1/P1002/P1002.preprocessedtest/dfile_rall.1D -regress_apply_mot_types demean deriv -regress_extra_ortvec ${stim_times_dir}cwm.1D ${stim_times_dir}ccsf.1D -regress_extra_ortvec_labels cwm ccsf

Thank you very much in advance!
Carolin
Subject Author Posted

How to get R^2 stats for noise model in resting state using afni_proc.py ?

carolin31 March 30, 2021 01:38PM