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pnlbwh / CNN-Diffusion-MRIBrain-Segmentation

CNN based brain masking
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Which volume is extracted as b0? #6

Closed tashrifbillah closed 4 years ago

tashrifbillah commented 4 years ago

@SenthilCaesar @suheyla2

Can you tell me which bvalue is used in extracting b0 image here?

Please see standard PNL way of extracting b0 image here and let me know which one is relevant to this project.

suheyla2 commented 4 years ago

Dwiextract extracts all bzeros. Senthil was later taking an average of the b0s.

-ave option with default threshold would work.

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Can you tell me which bvalue is used in extracting b0 image herehttps://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/blob/master/pipeline/preprocessing.py#L129?

Please see standard PNL way of extracting b0 image herehttps://github.com/pnlbwh/pnlNipype/blob/master/docs/TUTORIAL.md#i-baseline-image and let me know which one is relevant to this project.

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tashrifbillah commented 4 years ago

Fixed by https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/commit/c18b5f5bc51b955a07e55b52e35f9b5ea0528a0f