Slice timing in spinal cord fMRI


I’m writing a review on spinal fMRI data processing (addressing reviewers comments), and I’m looking into the application of slice timing correction for spinal fMRI data. I revisited the following publications:

The Eippert/Kong articles thoroughly describe methods for incorporating slice-specific nuisance regressors (based on external pulseOx and respiratory signals), but I don’t find any mention of slice-timing correction for the underlying BOLD signal, for all the above articles.

The Barry et al. article looks at within-slice correlations, so I guess slice timing correction was not needed there, but in general, what is the recommended approach for slice-timing correction in spinal fMRI time series?

Any thoughts/references would be appreciated :blush:


1 Like

Hi @jcohenadad - I did not use slice timing correction in the preprocessing of my 7T data because they were acquired with a 3D slab excitation and thus all slices were essentially acquired at the same time (or, perhaps more accurately, within the same temporal interval). I currently have a manuscript under review that acquired data using single-shot EPI and we did perform slice timing correction on those data (though the impact was presumably minor since the TR was quite reasonable at 2 sec). Hope this helps! -Rob

1 Like

Hi @jcohenadad

We did not use slice timing correction for our 3T spinal cord fMRI data as well. For task fMRI, it is not recommended to use slice timing in FSL, rather people would use temporal derivatives instead. That’s what we used in the GLM, to account for both slice timing and different HRF. For resting state data, we also used FEAT and GLM for pre-processing & physiological noise correction, again temporal derivatives was included.

Recently for our new data with ZOOMit or multi-band, we are exploring how different pre-processing strategies change results, we found that actually slice timing could improve results in terms of TSNR, activation and connectivity. We might recommend to use it in the future.



1 Like

@Yazhuo_Kong i’m not sure i understand why slice timing is not recommended for task fMRI, and how temporal derivatives can address this issue. E.g., in your approach, the nuisance regressors (cardiac, resp), include slice timing information, and therefore are slice-specific. But these are only the nuisance regressors, not the actual task-related BOLD signal, which would still have a different timing across slices, right? Same argument for resting-state: we could assume that neuronal connectivity is fast (and independent of) compared to slice timing acquisition, therefore correlations made across slices should account for this temporal offset :thinking: