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Hi Carlotta, You should register your functional data to your structural image, and register the structural image to the MNI152 template (which is in the same space as the Harvard-Oxford cortical atlas). You can then invert the registration transformations to take the atlas into the space of your functional data. All of this is covered in the FSL course registration practical: https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/registration/index.html Once you have the atlas image in functional space, you can use fslmeants to extract the time courses. Cheers, Paul On 29/11/2018, Carlotta Fabris <[log in to unmask]> wrote: > Hi everyone! > > I have the harvard oxford cortical atlas and I would like to be able to > etract the rois and then extract the average time course from each roi. > > To do it I have to have my fMRI signal and the atlas in the same dimension, > so how can I register the atlas to the fMRI? I know I have to use flirt but > when I tried it didn't work correctly. > > Also some suggestions on the rest of the process to follow to extract the > time course? > > Thank you, > Carlotta. > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1