tedana.combine
.make_optcom¶
-
make_optcom
(data, tes, adaptive_mask, t2s=None, combmode='t2s', verbose=True)[source]¶ Optimally combine BOLD data across TEs, using only those echos with reliable signal across at least three echos. If the number of echos providing reliable signal is greater than three but less than the total number of collected echos, we assume that later echos do not provided meaningful signal.
- Parameters
data ((S x E x T)
numpy.ndarray
) – Concatenated BOLD data.tes ((E,)
numpy.ndarray
) – Array of TEs, in seconds.adaptive_mask ((S,)
numpy.ndarray
) – Array where each value indicates the number of echoes with good signal for that voxel. This mask may be thresholded; for example, with values less than 3 set to 0. For more information on thresholding, see make_adaptive_mask.t2s ((S [x T])
numpy.ndarray
or None, optional) – Estimated T2* values. Only required if combmode = ‘t2s’. Default is None.combmode ({‘t2s’, ‘paid’}, optional) – How to combine data. Either ‘paid’ or ‘t2s’. If ‘paid’, argument ‘t2s’ is not required. Default is ‘t2s’.
verbose (
bool
, optional) – Whether to print status updates. Default is True.
- Returns
combined ((S x T)
numpy.ndarray
) – Optimally combined data.
Notes
This function supports both the
't2s'
method 1 and the'paid'
method 2. The't2s'
method operates according to the following logic:Estimate voxel- and TE-specific weights based on estimated :
Perform weighted average per voxel and TR across TEs based on weights estimated in the previous step.
References
- 1
Posse, S., Wiese, S., Gembris, D., Mathiak, K., Kessler, C., Grosse‐Ruyken, M. L., … & Kiselev, V. G. (1999). Enhancement of BOLD‐contrast sensitivity by single‐shot multi‐echo functional MR imaging. Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine, 42(1), 87-97.
- 2
Poser, B. A., Versluis, M. J., Hoogduin, J. M., & Norris, D. G. (2006). BOLD contrast sensitivity enhancement and artifact reduction with multiecho EPI: parallel‐acquired inhomogeneity‐desensitized fMRI. Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine, 55(6), 1227-1235.
See also
tedana.utils.make_adaptive_mask()
The function used to create the
adaptive_mask
parameter.