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Does anyone know how to skip using certain template files in the preprocessing package? Specifically, our lab does not have any vascular mask for our rodent atlas. Leaving out the --vascular_mask argument entirely does not work as it will then default to using the vascular mask provided in the docker container. |
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Replies: 2 comments 4 replies
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I believe in the current design, vascular masks are required, so you have a few options:
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The parameter for each template mask is non-optional (a mask must be provided), but you do not need to provide an 'accurate' mask if you are not using any of those for confound correction (i.e. regression of WM/CSF or vascular signal, or using ICA-AROMA which requires CSF mask). Instead, I recommend providing the brain mask instead as replacement, and the pipeline will run smoothly. |
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The parameter for each template mask is non-optional (a mask must be provided), but you do not need to provide an 'accurate' mask if you are not using any of those for confound correction (i.e. regression of WM/CSF or vascular signal, or using ICA-AROMA which requires CSF mask). Instead, I recommend providing the brain mask instead as replacement, and the pipeline will run smoothly.