Dear all,

I m trying to do all the pre processing using the command line and I have different some scripts for that. However I m not entirely sure of the pre-processing pipeline. Is it like this as below ?

mcflirt (EPI time series motion correction)

flirt (registration of functional to anatomical)

spatial smoothing

intensity normalization

highpass filtering

melodic

Can I skip high pass filtering (or any other of the previous steps) if I do melodic ?

I also couldnt find specific commands for spatial smoothign or highpass filtering; do I have to use fslmaths to do these ? can somebody please tell the detailed options ?

If I try using GUI for any ONE of these tasks; I cannot disable the rest of the options. Is there some way to do that ?

Thanks a lot

best

Qasim

Qasim Bukhari

Research Assistant and Doctoral Candidate

Institute for Biomedical Engineering

ETH and University Zurich

Wolfgang-Pauli-Strasse 27, HIT E22

webpages: MR-page

http://www.biomed.ee.ethz.ch/people/sybukhar