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Hi, It looks like your template fsf is for a higher-level analysis, in this case you will actually need to add the extra EVs individually to the fsf. This is a little tricky to manually - but you can get an idea of what to do by looking at the changes to a design.fsf when these EV’s are added. If you also have lower-level designs, then a call of the form feat_model <design_name_root> [confound matrix text file] Should add in extra EVs. Hope this helps, Kind egards Matthew -------------------------------- Dr Matthew Webster FMRIB Centre John Radcliffe Hospital University of Oxford On 10 Apr 2019, at 14:55, ACarroll <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi, Checking back on this - any thoughts are helpful! I have attached an example design.fsf that I am using (compressed in order to not exceed max message size), along with a contrast file that is the result of saving the design via the GUI (i.e. design_MANUAL.con) and a contrast file that is the result of running "feat_model design" (i.e. design_CL.con). The design_MANUAL.con file contains the correct information, and I am hoping to get some help on figuring out why using the command line does not correctly populate NumWaves or the contrast matrix dimensions. I wonder if the command line is not correctly referencing the confound EV .txt file. Thank you! ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 <design.fsf.zip><design_MANUAL.con><design_CL.con> ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1