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.

On 18 Oct 2018, at 16:06, Carlotta Fabris <[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!

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-----
Dr Janine Bijsterbosch
Postdoctoral Researcher
FMRIB Centre, University of Oxford
John Radcliffe Hospital
Oxford, United Kingdom
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