Create script to extract signal statistics for each class - Githubissues

neuropoly / totalspineseg

Segmentation of vertebrae, intervertebral discs, spinal cord and CSF from MRI images.

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Create script to extract signal statistics for each class #3

Closed jcohenadad closed 1 year ago

jcohenadad commented 1 year ago

I suggest we write a simple Python script to do that. The algorithm is as follows:

Initialize a pandas dataframe (row: subject, column: mask)
Loop across BIDS structure (sub-*)
For each subject (sub-xxx), open the image with nibabel
Loop across the masks under derivatives/manual_masks/sub-xxx/anat/*
For each mask, compute the mean and STD (use numpy.mean(mask)) and update the dataframe
At the end, save dataframe as CSV.

yw7 commented 1 year ago

@jcohenadad Is it ok to put the code in master branch under 'scripts'? or should we create a branch for development?

jcohenadad commented 1 year ago

Is it ok to put the code in master branch under 'scripts'? or should we create a branch for development?

Create a branch specific to this issue, eg: yw/extract-signal and open a PR so I can review the code. Let's do code development with professional standard (ie: with at least one code review).