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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August 02, 2013 08:40AM
Dear Afni experts, as you can appreciate from the picture, there seems to be a strong trend in my time series, which I don't want to see in my plots.
This is the command (is used a very high polynomial degree because the scans are 1200repetitions)

3dDeconvolve -input pb04.$subj.r*.scale+orig.HEAD \
-censor motion_${subj}_censor.1D \
-polort 20 \
-num_stimts 7 \
-stim_times 1 stimuli/onset_times_HRF_240s_baseline.txt \
'CSPLINzero(0,20,8)' \
-stim_label 1 electro \
-stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll \
-stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch \
-stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw \
-stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS \
-stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL \
-stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP \
-iresp 1 iresp_electro.$subj \
-sresp 1 sresp_electro.$subj \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subj \
-errts errts.${subj} \
-bucket stats.$subj

The Question:
Is it supposed to look like that? Would I have to generate a contrast between my stimulus vector and the 20 polort vectors of the X matrix in order to see the cleaned data that I would like to plot (horizontal lines with the low frequencies regressed out, only stimulus related signal + noise) ? How can I do this using -gltsym when the polort vectors have no label?




the graph shows the all_runs bucket overlayed with the fitts bucket.
Subject Author Posted

How to display data without trends?

paranoidandroid August 02, 2013 08:40AM

Re: How to display data without trends?

gang August 02, 2013 03:58PM