Hi Luca,
Did you try the command as mentioned above?
You should run the subject with SVReg and with BrainSuiteAtlas1 as the atlas. Then run
/home/ajoshi/BrainSuite16a1/svreg/bin/svreg_apply_map.sh subname.svreg.inv.map.nii.gz fa_map.nii.gz out_fa.nii.gz /home/ajoshi/BrainSuite16a1/svreg/BrainSuiteAtlas1/mri.bfc.nii.gz