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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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ptaylor
January 18, 2019 05:20PM
Hi, Brady-

Re. censor things:
I was just looking through an proc* script output for afni_proc.py that has been run recently. I think you want to look at the start of the regress block part of the script-- in my proc* script, there were lines like this: 
# ================================ regress =================================

# compute de-meaned motion parameters (for use in regression)
1d_tool.py -infile dfile_rall.1D -set_nruns 1                            \
           -demean -write motion_demean.1D

# compute motion parameter derivatives (just to have)
1d_tool.py -infile dfile_rall.1D -set_nruns 1                            \
           -derivative -demean -write motion_deriv.1D

# create censor file motion_${subj}_censor.1D, for censoring motion 
1d_tool.py -infile dfile_rall.1D -set_nruns 1                            \
    -show_censor_count -censor_prev_TR                                   \
    -censor_motion 0.2 motion_${subj}

# combine multiple censor files
1deval -a motion_${subj}_censor.1D -b outcount_${subj}_censor.1D         \
       -expr "a*b" > censor_${subj}_combined_2.1D

The complete censor file depends also on the outlier calc from before, too, in the "outcount" section, where I had something like: 
# catenate outlier censor files into a single time series
cat rm.out.cen.r*.1D > outcount_${subj}_censor.1D

Hope that's useful, and please ping back with any follow-up questions.

--pt
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Issue with stats in afni_proc.py Attachments

wilxl8 January 17, 2019 02:48PM

Re: Issue with stats in afni_proc.py

Peter Molfese January 17, 2019 02:55PM

Re: Issue with stats in afni_proc.py

rick reynolds January 17, 2019 05:03PM

Re: Issue with stats in afni_proc.py

ptaylor January 17, 2019 06:13PM

Re: Issue with stats in afni_proc.py

wilxl8 January 18, 2019 11:42AM

Re: Issue with stats in afni_proc.py

ptaylor January 18, 2019 01:41PM

Re: Issue with stats in afni_proc.py

wilxl8 January 18, 2019 04:26PM

Re: Issue with stats in afni_proc.py

ptaylor January 18, 2019 05:20PM

Re: Issue with stats in afni_proc.py

Peter Molfese January 18, 2019 08:08PM