Hi Yan, I can speak for the preprocessed DTI data that it is the data with all of the preprocessing pipelines described in (Glasser et al. 2013).
Depending on what you want to analyze, it could be in your benefit to start at the preprocessed data. For DTI, they have already corrected the distortions as well as the eddy currents so the data has had it's motion correction completed already. With the preprocessed data you could immediately put the data in FSL and start at DTIFIT, TBSS or otherwise. However, as described in the paper, BedpostX has not been run on the data. Cheers, _______________________________________ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia Date: Wed, 1 Oct 2014 10:24:24 -0500 From: "Jennifer Elam" <[email protected]> Subject: Re: [HCP-Users] [HCP-Info] [Contact Form]: about data To: '??' <[email protected]> Cc: [email protected], [email protected], [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="gb2312" In the HCP diffusion acquisition protocol, we collect six diffusion series (each set of directions in LR and RL phase encoding directions), and that is reflected in the unprocessed data. The HCP diffusion preprocessing pipeline starts by intensity normalizing the mean b0 image across the six diffusion series. These phase encoding direction reversed b0 pairs are used to estimate the EPI distortion using the ?topup? tool ( Andersson et al., 2003) in FSL5. In the preprocessed fMRI series data, each rfMRI scan was collected with each of the two phase encoding directions. The preprocessing is done ?within run? rather than across runs, so that is why you see data for the 4 scans: (REST1, REST2, for LR and RL). The single band reference scan (SBRef) serves as the reference for motion correction, EPI distortion correction and for more accurate EPI to T1w registration. I would recommend you look at Glasser <http://www.sciencedirect.com/science/article/pii/S1053811913005053> et al. 2013 for more information on the diffusion and functional preprocessing. Best, Jenn Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 [email protected] www.humanconnectome.org<http://www.humanconnectome.org> From: ?? [mailto:[email protected]] Sent: Tuesday, September 30, 2014 4:31 PM To: Jennifer Elam Cc: [email protected]; [email protected]; [email protected] Subject: Re: Re: [HCP-Users] [HCP-Info] [Contact Form]: about data But I still feel confused. You means I can use any group data to get the brain fiber such as L-R and 95 directions? But why are there only one data in processed data? In addition, I found in fMRI data, you keep the L-R and R-L data in both unprocessed data and processed data. So if I deal with fMRI, can I analyze any group data. What different can I get? Last, I find a lot of *_SBRef.nii in the unprocessed data. I don't know what this data describe? -----????----- ???: "Jennifer Elam" <[email protected]> ????: 2014?10?1? ??? ???: [email protected] ??: [email protected], [email protected] ??: Re: [HCP-Users] [HCP-Info] [Contact Form]: about data Hi Yan, We provide our diffusion data in separate unprocessed and minimally preprocessed data packages so that users need only download one or the other, depending on whether they want to process data from the beginning or proceed with analysis steps after normal preprocessing steps have been applied. Others on the HCP-users list may be able to help you with your other questions. Please sign up for the HCP-users email list <http://humanconnectome.org/contact/#subscribe> and ask your questions in that forum so that all can benefit from the responses. Best, Jenn Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 [email protected] www.humanconnectome.org<http://www.humanconnectome.org> -----Original Message----- From: [email protected] [<https://www.mail.ubc.ca/owa/UrlBlockedError.aspx>mailto:info-bounces@humanconnectome. org] On Behalf Of [email protected] Sent: Saturday, September 27, 2014 10:19 AM To: [email protected] Subject: [HCP-Info] [Contact Form]: about data Name: yan tang Email: <mailto:[email protected]> [email protected] Institution: TTU Subject: [Contact Form]: about data Comments: I am beginner. I want to download the DTI data but are conflused by the processed data and unprocessed data. 1)The unprocessed data contains the NIFTI-formatted pairs (L-R, R-L) of diffusion scans for all directions (95,96,and 97). And processed data only include diffusion weighting (bvals), direction (bvecs), time series, brain mask, and a file (grad_dev.nii.gz). Why? what did you only keep? 2)In the processed data, whether the file of *_SBRef.nii describe the B0? 3)I download the processed data, but I couldn't use the Micron to open the data.nii. Why? I download two subjects. Both subjects couldn't be opened _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
