I made this question some time ago in the FSL forum and they I found out the answer by myself, so I just wanted to share in case someone is interested in doing this.

If you use the field map method for fMRI BOLD by using an opposite sequence in the phase direction (opposite blip), you can use FSL topup to create the Field Map in Hz.

Here is the method:
 
[url=https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1606&L=fsl&P=R5352&1=fsl&9=A&J=on&X=8C2FAA6D38C85511B3&Y=egarza%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4]https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1606&L=fsl&P=R5352&1=fsl&9=A&J=on&X=8C2FAA6D38C85511B3&Y=egarza%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4[/url]

In summary, run "topup" in FSL, get the Field in Hz using the --fout flag and correct readout time, load the field file in SPM Fieldmap Toolbox into and use the EPI to create the VDM file needed in CONN.

Kind regards

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Eduardo Garza-Villarreal
National Institute of Psychiatry, Mexico City, Mexico