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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October 23, 2014 11:06AM
Hi Afni experts,
I am looking to run ICA analysis on data previously processed with afni. I know I will have to make some modifications regarding how to analyze and needed guidance on one particular aspect regarding motion scrubbing.

Previously I would run through afni_proc.py and get a file of combined TRs to delete from extreme outliers and motion that I would incorporate at the end using 3dDeconvolve with my seed time series. With ICA I would not be using a seed obvioulsy but is it still valid to delete these timepoints for this type of analysis? Furthermore, would I be able to take my processed file(despike, ricor, slice time,motion correction, B0, anaticor, smooth - no bandpassing for ICA) and run through 3dDeconvolve without any stims in order to delete these outliers with the following command (if this is not correct please let me know what the command would be) or is there a better way to do this scrubbing (ie incorporate somehow in @Anaticor or another tool to censored timepoint info without running GLM)?

3dDeconvolve -input $rest_file \
-polort $pol \
-censor $censor_file \
-tout -rout -fitts fit_${sub} \
-bucket $sub.anaticor.smooth.censor

The bucket file is usually what I would use for seed based as it is the output comparison of a seed and the voxel timeseries, however, I am not sure if that is the appropriate output in this case to feed into melodic or another tool (if afni has for ICA).

Thanks,
Ajay
Subject Author Posted

ICA analysis and motion scrubbing (censor timepoints) using 3dDeconvolve

AjaySK October 23, 2014 11:06AM

Re: ICA analysis and motion scrubbing (censor timepoints) using 3dDeconvolve

rick reynolds October 24, 2014 12:46PM

Re: ICA analysis and motion scrubbing (censor timepoints) using 3dDeconvolve

AjaySK October 29, 2014 02:33PM