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Hi, I’m afraid that at the moment there is no easy way to avoid re-running things in the VBM scripts. The only way to do it is to edit the script to copy in the previously created files rather than running FAST. However, this is only a good option if you are familiar with scripting. All the best, Mark From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of "Rachel E." <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Tuesday, 28 July 2015 17:51 To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: [FSL] fsl_anat and VBM Hi All, I am trying to do VBM analysis on my data set. I ran into a lot of problems getting good extractions with fslvbm_1_bet but used fsl_anat and was able to get really good extractions of nearly all my subjects. Now I am ready to move forward. I see that fsl_anat spits out a lot of the data that fslvbm_2_template generates. Any suggestions on how to take my outputs from fsl_anat and input them back into the VBM pipeline beginning with fslvbm_2_template. Thanks! -Rachel