FSL feat_model with confound EVs


I am trying to run many subjects through Feat level 1 on the commandline and I want to include “estimated high-pass filter cutoff” values based on the design matrix (which are slightly different for each subject).

I’m using a template .fsf file (with the high pass filter cutoff set to 9999 as suggested in another thread on FSL archives), changing the relevant info (e.g., file paths) for each subject, and using feat_model to generate a design.mat file to be used as the input for cutoffcalc, which estimates that high-pass filter cutoff value.

The problem I am running into is that feat_model generates a design.mat file that does not include the additional confound EVs (i.e., extra motion parameters) specified in my .fsf template and thus gives a very different value than if I estimate it on the Feat GUI (e.g., cutoff= 480 versus 90). Is there any way to include those confound EVs in the design.mat without having to load each subject into the GUI manually?


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I actually figured it out: I just needed to specify the confound EV matrix text file in the feat_model command (example: feat_model design.mat my_confound_EVs.txt)

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