Re: [HCP-Users] Finding the B0 Image

[Harms, Michael]

Yes, the first volume should be *one* of the b=0 images (check the bvals file).  Note that b=0 volumes are interspersed throughout the acquisition. For the preprocessed data, all the available dMRI data is concatenated into that single data.nii.gz file (and the bvec, bvals to match).  The preprocessed data is also corrected for motion, eddy currents, and transformed into that subject's T1w space (with appropriate adjustment to the bvecs).  The preprocessed data is definitely the recommended data to start with. 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: Connectome Issues <iss...@humanconnectome.org> Date: Monday, October 13, 2014 11:45 AM To: "Cunningham, Samantha (NIH/NIAAA) [F]" <samantha.cunning...@nih.gov>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Cc: "supp...@humanconnectome.org" <supp...@humanconnectome.org> Subject: Re: [HCP-Users] Finding the B0 Image Fowarded issue 2 of 2.  On Tue, Oct 7, 2014 at 3:48 PM, Cunningham, Samantha (NIH/NIAAA) [F] <samantha.cunning...@nih.gov> wrote: Hello, I am currently trying to process an unprocessed DWI dataset from the Human Connectome database in FSL (Subject 1003070 from  WU-Minn HCP Data à 500 subjects à 10 unrelated subjects) and have two questions:   1.       Is the first image in the “100307_3T_DWI_dir97_LR.nii.gz” file the b0 image? 2.       For the preprocessed version of the dataset, does the data.nii.gz file include all 3 datasets (95 directions, 96 directions, and 97 directions), or only one of these?   Thank you for your help! Samantha Cunningham, Ph.D. Postdoctoral Fellow National Institutes of Health|NIAAA|LNI samantha.cunning...@nih.gov   _______________________________________________ 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