That is okay. FSL BBR is only used to initialize FreeSurfer BBR anyway. Peace,
Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Parvathaneni, Prasanna" <[email protected]<mailto:[email protected]>> Date: Thursday, June 21, 2018 at 12:59 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] DiffusionToStructural issue with epi_reg_dof Hello, We are trying to process our custom diffusion dataset by adapting DiffusionToStructural.sh script from HCP. However when running below command its failing at the BBR step >> ${GlobalScripts}/epi_reg_dof --dof=6 --epi=$DATADIR/b0.nii.gz >> --t1=$PROCESSDIR/T1w/T1w.nii.gz >> --t1brain=$PROCESSDIR/$i/T1w/T1w_brain.nii.gz --out=$DIFFUSIONDIR/bo_t1 with following error ERROR::set_bbr_seg: could not find any boundary points! > WARNING:: Found NaN in BBR cost (2) And one of the outputs (fast_pve_2) from FAST command seems to be empty which is causing to have empty fast_wmseg file. If we supply a wmseg file (using freesurfer generated segmentation files), it seem to be working fine. Can you please suggest if you see any issues with this approach or if you have other suggestions. Thanks, Prasanna _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
