The issue with using FreeSurfer 6.0 in the HCP Pipelines is that some aspects of the surface generation on HCP-Young Adult data were better using the FreeSurfer 5.3.0-HCP release. We are in the process of checking the performance of a beta version of FreeSurfer 6.X on HCP-YA data.
If you use FreeSurfer 6.0, our advice is that you check your surfaces (which you should be doing anyway!), and decide if you are satisfied with them. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy Coalson <tsc...@mst.edu> Date: Tuesday, June 19, 2018 at 3:22 PM To: "Parvathaneni, Prasanna" <prasanna.parvathan...@vanderbilt.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP processing with ciftify requirements On Sat, Jun 16, 2018 at 8:36 PM, Parvathaneni, Prasanna <prasanna.parvathan...@vanderbilt.edu<mailto:prasanna.parvathan...@vanderbilt.edu>> wrote: Hi All, Thank you for suggesting “ciftify” on non-HCP datasets. We are trying to run HCP pipeline using “ciftify" tool on our custom dataset and have few questions * For running recon-all can we use Freesurfer v6. Suggested version for HCP (Freesurfer 5.0.3_HCP) seem to have compatibility issues on Ubuntu 16.08 as mentioned in below thread https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04158.html The ciftify pipeline is not the HCP pipelines. It is a workaround for studies that don't follow HCP acquisition guidelines, to be able to get some (but not all) of the advantages of the HCP preprocessing methods. I would expect that it can accept freesurfer v6 output, but I don't know for sure. * Do you have any scripts for transforming diffusion data that is aligned to subject T1 into “cifti” space similar to ciftify_subject_fmri for FMRI data We haven't released tractography results for HCP data due to unsolved issues with tractography in general ("gyral bias"). You can run tractography using surface-based counting, and surface-based cortical results make sense to convert to standard grayordinate space. However, the diffusion/fiber direction information is most definitive in the white matter, while our standard grayordinate space only covers gray matter, so it would not make sense to convert that into grayordinate space. Appreciate your feedback. Thanks Prasanna _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
