Yes, in DiffPreprocPipeline_PostEddy.sh you’ll need to use “--combine-data-flag=2”
Also, I want to caution you about collecting only half of the total dMRI data that we collected in the UMN Lifespan piloting. There is a reason that we collected a full 20 min of dMRI when using 1.5 mm resolution. Before you collect less total data (at that same spatial resolution), I would run some piloting to check if reducing the amount of data is sufficient to generate good quality for your measures of interest. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders 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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, May 23, 2017 at 9:01 AM To: HMZ <hmz...@163.com<mailto:hmz...@163.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "g...@pku.edu.cn<mailto:g...@pku.edu.cn>" <g...@pku.edu.cn<mailto:g...@pku.edu.cn>>, Jia-Hong Gao <j...@pku.edu.cn<mailto:j...@pku.edu.cn>> Subject: Re: [HCP-Users] Question about DWI protocol Yes as long as you have phase reversed b0s you can have the DWIs have unique directions. The HCP diffusion pipeline might need modification to accommodate that. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of HMZ <hmz...@163.com<mailto:hmz...@163.com>> Date: Tuesday, May 23, 2017 at 2:14 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "g...@pku.edu.cn<mailto:g...@pku.edu.cn>" <g...@pku.edu.cn<mailto:g...@pku.edu.cn>>, Jia-Hong Gao <j...@pku.edu.cn<mailto:j...@pku.edu.cn>> Subject: [HCP-Users] Question about DWI protocol Dear HCP experts, This is Meizhen Han from Center for MRI research at Peking University in China. I'm writing for seeking a solution for the problem we encountered during the application of HCP MRI sequence on our recent research. I noticed that HCP acquired DWI data twice with reversed phase direction in order to calculate the fieldmap, which I think is perfect but a little time-consuming especially when 2 or 3 gradient tables are used. I'm wondering whether it is OK to acquire one phase encoding direction of one gradient table and reversed direction of another gradient table. Taking Lifespan DWI protocol of UM for example, can we only get DWI_dir98_AP and DWI_dir99_PA, and then take out b0 images in both files to caculate fieldmap? Any relevant information and idea would help a lot. Thank you very much! Looking forward to your reply. -- Best Regards! Meizhen Han -- Meizhen Han PhD Candidate Center for MRI Research Peking University Beijing, China _______________________________________________ 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<mailto: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
