Hi, Ah, sorry I think I had the tool names mixed up in my earlier message. You have to generate the design.mat file from your text file using the Glm GUI (see screenshot below). This will allow you to save your design (i.e. it will generate the design.mat file for you), which you then enter into fsl_glm. Best wishes, Janine [cid:F0627B6F-0FD9-4AF8-8AC7-4CE709B1A089@fmrib.ox.ac.uk] On 18 Oct 2018, at 16:06, Carlotta Fabris <[log in to unmask]<mailto:[log in to unmask]>> wrote: This is the file I am using as input: fsl5.0-fslinfo filtered_func_data.nii.gz data_type FLOAT32 dim1 64 dim2 64 dim3 36 dim4 260 datatype 16 pixdim1 3.000000 pixdim2 3.000000 pixdim3 4.000000 pixdim4 1.999999 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ And the command I use is: fsl_glm -i filterend_func_data.nii.gz -d design.txt -o filtered_func_data_regressed.nii.gz I guess the error is in the design.txt but I am really not sure how to fix it. Thanks for everything! ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ----- Dr Janine Bijsterbosch Postdoctoral Researcher FMRIB Centre, University of Oxford John Radcliffe Hospital Oxford, United Kingdom [log in to unmask]<mailto:[log in to unmask]> ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1