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Mapss T2 calculation requires mask[BUG] #136

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gattia opened this issue Oct 27, 2023 · 0 comments
Open

Mapss T2 calculation requires mask[BUG] #136

gattia opened this issue Oct 27, 2023 · 0 comments

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@gattia
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gattia commented Oct 27, 2023

Describe the bug
A clear and concise description of what the bug is.

# only calculate for focused region if a mask is available, this speeds up computation
mask = tissue.get_mask()
if mask_path is not None:
mask = (
fio_utils.generic_load(mask_path, expected_num_volumes=1)
if isinstance(mask_path, (str, os.PathLike))
else mask_path
)

The above section of code shows that the tissue class is required for the T2 generation to go through. If the tissue class is not present then .get_mask() will fail (None type does not have the function). However, tissue class is meant to be optional.

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