Re: [HCP-Users] Diffusion processing

[Harms, Michael]

Please reply to the group so that others can follow the conversation. frames=volumes=directions. They are acquired as 95,96,97 because a given number of total directions can only have a single entry in the file that specifies the gradient table.  i.e., you can't have 3 x 96 different sets of directions in the gradient table, thus 95,96,97 instead. 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: Mahmoud <zeydab...@gmail.com> Date: Monday, December 14, 2015 9:07 AM To: "Harms, Michael" <mha...@wustl.edu> Subject: Re: [HCP-Users] Diffusion processing Dear Michael, By "frames" you mean "volumes=directions" or "slices" ? I would assume you meant volumes, If so, I still don't know why they are not all acquired in 96 frames? Thank you! Mahmoud On Mon, Dec 14, 2015 at 9:51 AM, Harms, Michael <mha...@wustl.edu> wrote: The dir{95,96,97} labels in the "raw" (unprocessed) NIFTI files represent the total number of frames acquired in that acquisition, including the b=0. 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: Mahmoud <zeydab...@gmail.com> Date: Monday, December 14, 2015 8:14 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Diffusion processing Dear HCP developers and users, >From what I understood for the HCP DTI dataset this is true: “Sampling in q-space includes 3 shells at b = 1000, 2000 and 3000 s/mm2. For each shell, 192 data points are obtained, corresponding to 90 diffusion gradient directions and 6 b = 0's acquired twice, with the phase encoding direction reversed for each pair (i.e. LR and RL pairs) “ Please correct me if I’m wrong. According to above, in total we should 6 datasets all has 96 (90+6) volumes but different PE direction and b-values. Would you please explain to me what does the HCP raw data naming convention means here? i.e. I don’t know why we should have 95, 96 ,and 97 directions? I do appreciate your elaboration. Thank you, Mahmoud _______________________________________________ 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.   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