Including lesion maps in BIDS dataset

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Nutsa Ninua

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Oct 17, 2022, 7:46:02 AM10/17/22
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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

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Oct 17, 2022, 8:00:30 AM10/17/22
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Remi Gau

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Oct 17, 2022, 8:33:03 AM10/17/22
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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

Nutsa Ninua

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Oct 18, 2022, 4:24:04 AM10/18/22
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Thank you! 
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