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DOC: Add warning about slice timing correction in output documentation. #2502

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merged 11 commits into from
Sep 8, 2021
12 changes: 12 additions & 0 deletions .zenodo.json
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"name": "Ghosh, Satrajit S.",
"orcid": "0000-0002-5312-6729",
"type": "Researcher"
},
{
"affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
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"name": "Schaefer, Theo A.J.",
"orcid": "0000-0003-4102-559X",
"type": "Researcher"
},
{
"affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
"name": "Nitsch, Alexander",
"orcid": "0000-0002-5740-9451",
"type": "Researcher"
}
],
"creators": [
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7 changes: 7 additions & 0 deletions docs/outputs.rst
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sub-<subject_label>_[specifiers]_AROMAnoiseICs.csv
sub-<subject_label>_[specifiers]_desc-MELODIC_mixing.tsv

.. caution::
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Slice timing correction in fMRIPrep is referenced to the middle slice which leads to a time shift in the volume onsets by 0.5 TR (for example, assuming a TR of
2 s, original onsets of 0, 2 and 4 s would be shifted to 1, 3 and 5 s). In case you did not disable slice timing correction, you should consider this shift in
subsequent analyses (e.g. general linear modeling). For example, when specifying a first-level model, you should set parameters in your software package or
first-level model function accordingly (e.g. select middle slice as reference). Alternatively, you could manually adjust the volume onsets (e.g. as mentioned in
the example above from [0, 2, 4] to [1, 3, 5]) or the event onsets accordingly.
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Confounds
---------
The :abbr:`BOLD (blood-oxygen level dependent)` signal measured with fMRI is a mixture of fluctuations
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