Hmmm. What is the specific error message that you are getting? In the 4.0.0 pipelines, the necessary custom scripts that you mentioned are provided with the pipeline distribution, and are contained in the HCPpipelines/FreeSurfer/custom directory.
It sounds like you don’t have something configured correctly. i.e., perhaps your $HCPPIPEDIR variable is not actually set to the location of the 4.0.0 distribution? 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 Aaron C <aaroncr...@outlook.com> Date: Friday, May 17, 2019 at 11:05 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] A question about the HCP pipeline 4.0.0 Dear HCP experts, I have a question about the HCP pipeline 4.0.0. When using FreeSurferPipelineBatch.sh, it cannot find recon-all.v6.hires, conf2hires, and longmc. Is there a specific version of FreeSurfer 6.0 for HCP? Thank you. _______________________________________________ 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
