The HCP has received requests for slice-timing parameters for the HCP fMRI data and, therefore, we are providing this information with some background as to why the HCP functional preprocessing pipeline pipeline does not include slice-timing correction (see Smith et al. "Resting-state fMRI in the Human Connectome Project" NeuroImage, vol. 80, pp. 144-168, Oct. 2013 and Glasser et al. “The minimal preprocessing pipelines for the Human Connectome Project” Neuroimage, vol. 80, pp. 105–124, Oct. 2013).
The slice timing of the HCP fMRI is non-trivial due to the multi-band nature of the acquisition (MB=8 was used on rfMRI and tfMRI). Examples of the timing for both an even or odd number of total slices, and differing MB factors are provided in the following file. : CMRR_MB_Slice_Order.pdf We generally followed these guidelines with the HCP data. More information and the
The current version of the MB sequence is available here: https://www.cmrr.umn.edu/multiband/
However, our The TR of acquisition for HCP fMRI is quite short at 0.72 sec. Because of the short TR, HCP consortium members felt the value of slice timing correction (STC) for HCP fMRI data is very limited, therefore . Therefore we have opted not to slice-time correct the task or resting state data in our HCP processing.
If you still feel it is necessary to do slice timing correction, you will need to account for the non-trivial nature of slice acquisition in the MB sequencesacquisitions. Although we aren't distributing dicoms DICOMs (due to their size and the presence of private health privileged information in them), we do have slice time order/acquisition information available in the original dicom DICOM headers.
In the following text file, we have extracted the slice timing order info for an exemplar subject. Note that these values are only accurate to 2.5 ms:
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