Hi Jenn, Thank you very much for pointing me to the wiki. So far I haven't used STC but I may add it in the future to see if it makes a difference.
Best, Martin On 12/13/13 16:21, Jennifer Elam wrote: > 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+acquisition+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 . 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 > > [email protected] <mailto:[email protected]> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > -- 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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
