processing-scripts > motion outliers
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Feb 19, 2013  09:02 AM | Hsiao-Ying Wey
motion outliers
Dear experts,

I have been using these wonderful scripts happily. Thanks a lot for all the hard work.

I have a question regarding analyzing seed-based FC with motion outliers. Methods have been proposed to detect time-points with excessive motion (with both SPM and FSL), and marked such time-points as motion outliers. The way to incorporate these motion outliers into FC analysis is to use them as regressors of non-interest (i.e. confound EVs with 1 at motion time-point and 0 for the rest of the time series; if there are 4 motion outliers, there will be 4 columns in the design matrix in addition to the time-course of interests).

I was wondering if there is a easier way to incorporate the motion outliers into the script, especially in 6_sunglesubjectRSFC? Should I generate a ".mat" contrast file instead of the "ideal_file"? Could I still be using 3dfim+ or should I switch to 3dDeconvolve? It will be more complicated if I use FEAT in FSL to accomplish this task. Since I don't have a lot of experience in AFNI, I would really appreciate any suggestions!

Thank you so much for your help!

Feb 21, 2013  03:02 AM | Maarten Mennes
RE: motion outliers

thank you for liking our scripts :)

Unfortunately, I'm not fluent in AFNI either - I would suggest you try the afni forums in you want to go with afni. However, you could also try to implement it using FEAT. I'm not sure if it would be more complicated. You would have to make some changes to the 5_nuisance script to incorporate a .txt file that has your extra regressors. The latest version of FEAT let's you specify such file to read in multiple covariates at once. Once you have the txt file with your regressors, it would be a matter of running FEAT once manually so you have a working fsf. Then change the real input entries in the .fsf into generic ones (e.g., sub8503 becomes SUBJECT) and use that as your .fsf template. Then use sed, as in 5_nuisance - part 6, to replace SUBJECT with the actual subject you want to process.

e.g., you will see in 5_nuisance that we replace 'nuisance_model_outputdir' in /templates/nuisance.fsf for a proper subject output dir. You would just add a line for adding the motion regressors file.

Hope this helps,