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]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
