Hi Martin,
We have gathered information and fMRI slice timing order for an exemplar subject on a public wiki page for HCP fMRI slice-timing acquisition parameters <https://wiki.humanconnectome.org/display/PublicData/HCP+fMRI+slice-timing+a cquisition+parameters> . Hopefully this page has everything you need for your analysis. Another HCP consortium member will have to answer your question about the parameters to use with FSL's topup. 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 -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Martin Luessi Sent: Monday, December 09, 2013 2:43 PM To: [email protected] Subject: [HCP-Users] EPI distortion correction and slice-timing correction for fMRI data Dear HCP users, I'm working on using slightly different preprocessing steps for the resting-state fMRI data. However, I have some problems with determining how to perform the EPI distortion correction and slice-timing correction. Specifically: 1) What are the parameters to use with FSL's topup tool to obtain the warp field? I know this tool uses the field maps(e.g. 100307_3T_SpinEchoFieldMap_{LR, RL}.nii.gz) but it also needs additional parameters, i.e., acquisition parameters specified using "--datain" and a configuration specified using "--config". Does anyone know what parameters to use for the HCP data? Ideally, they should be the same as used for the minimally processed data as described in [1]. 2) What are the slice acquisition times to be used for slice-timing correction? I know that a SMS sequence with 8 simultaneous slices was used. However, so far I haven't been able to find at what time (relative to start of volume) each slice was acquired, which is necessary for slice-timing correction. Any help is appreciated. Regards, Martin Luessi [1] M. F. Glasser, S. N. Sotiropoulos, J. A. Wilson, T. S. Coalson, B. Fischl, J. L. Andersson, J. Xu, S. Jbabdi, M. Webster, J. R. Polimeni, D. C. Van Essen, and M. Jenkinson, "The minimal preprocessing pipelines for the Human Connectome Project.," Neuroimage, vol. 80, pp. 105-24, Oct. 2013. -- Martin Luessi, Ph.D. Research Fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 Fax: +1 617 726-7422 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at <http://www.partners.org/complianceline> http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ HCP-Users mailing list <mailto:[email protected]> [email protected] <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
