Including lesion maps in BIDS dataset

[Nutsa Ninua]

Hi everyone! 

Does anyone have experience with including lesion maps in NIFTII format in your dataset? Should it be part of the anat folder with a separate subfolder or included in derivatives? 

Best,

Nutsa

[Daniele Marinazzo]

Hi

we have it in the "derivatives"

https://openneuro.org/datasets/ds001226/versions/5.0.0

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[Remi Gau]

Several options:

- the derivatives section of the specification has a lesion label for the segmentation output:

https://bids-specification.readthedocs.io/en/latest/05-derivatives/03-imaging.html#common-image-derived-labels

- if you intend to use fmriprep, then it seems to follow the old BEP003 and puts it in the anat folder (as far as I understand)

https://fmriprep.org/en/stable/workflows.html#cost-function-masking-during-spatial-normalization

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Rémi Gau

[Nutsa Ninua]

Thank you!