Second Round of ACE Fixes #152
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Adds ability to number blobs in binary segmentation files. This allows for things such as counting unique blobs, filtering based on area, or computing stats.
Leave the datatype the same as the original to avoid the issue.
Changes made to processing in parallel and saving information in json file to speed up downstream processing
This is needed for using heatmap in a workflow. Otherwise, when the heatmap command is passed a None arg for `side` (if the workflow has a None arg for `side`), heatmap will fail with an error. Logic to handle this None arg exists in the heatmap script.
The arg for the treated directory was incorrect. It should match the arg for the control dir.
Variable `inclar` was not being used. It gets set manually and does not need to be an input to the function.
Update allows user to skip 0 slices if they'd like. Code would fail on 0 slices before.
`regionprops_table` not available in the version of `skimage` in `miracl`.
Arg is expected in int format (between 0 and 100) and instance seg expects it in float format (between 0.0 and 1.0).
Ace stats arg names were previously changed but were not propagated to the ace workflow.
Model outputs were not being handled correctly. Need to select foreground channel and apply softmax, otherwise threshold has no meaning (when we just compare foreground and background logits). We also need to discretize the values in a separate step than binarizing.
This commit handles all debugging and refactoring of the validate clusters script. Since the script was not in a workign condition before, this contains all debugging changes necessary to get the script working.
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validate clustersmodule. Validate clusters will count the neurons per cluster (from ACE stats) and compare it across all subjects.