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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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Nicholas Balderston
February 02, 2017 04:26PM
Hi everyone,

We collected multi-echo data on an N-back task. We preprocessed the data using the meica.py script, and then performed the first level analyses on the denoised timeseries. However, when we extract the betas from load-related regions, we see mostly negative betas, which is not what we predicted. One possibility is that we are somehow overfitting our baseline during 3ddeconvolve. Here's my question:


Given a dataset that has been denoised with a multi-echo ICA, what polort would you recommend using at the first level analysis?



Here's our 3ddeconvolve script for reference. 
3dDeconvolve \
-input ${subject}.run2.scale_al+orig.HEAD ${subject}.run3.scale_al+orig.HEAD \
-censor ${stmdir}/${subject}.task_censor.1D \
-ortvec ${stmdir}/${subject}.task.motion.1D motion \
-polort A \
-num_stimts 7 \
-stim_times 1 ${stmdir}/${subject}.shock.stimtimes.1D 'BLOCK(1,1)' \
-stim_times 2 ${stmdir}/${subject}.button.stimtimes.1D 'BLOCK(1,1)' \
-stim_times 3 ${stmdir}/${subject}.instruction.stimtimes.1D 'BLOCK(8,1)' \
-stim_label 1 "shock" \
-stim_label 2 "button" \
-stim_label 3 "instructions" \
\
-stim_times 4 ${stmdir}/${subject}.safeone.stimtimes.1D 'BLOCK(42,1)' \
-stim_times 5 ${stmdir}/${subject}.safethree.stimtimes.1D 'BLOCK(42,1)' \
-stim_times 6 ${stmdir}/${subject}.thrtone.stimtimes.1D 'BLOCK(42,1)' \
-stim_times 7 ${stmdir}/${subject}.thrtthree.stimtimes.1D 'BLOCK(42,1)' \
-stim_label 4 "safeone" \
-stim_label 5 "safethree" \
-stim_label 6 "thrtone" \
-stim_label 7 "thrtthree" \
-tshift \
-bout \
-fout \
-rout \
-tout \
-vout \
-x1D X.xmat.1D \
-xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts ${subject}.task.fitts \
-errts ${subject}.task.residuals \
-cbucket ${subject}.task.cbuck \
-bucket ${subject}.task.buck \
-jobs 16
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Multi-echo data and Polort

Nicholas Balderston February 02, 2017 04:26PM