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README.md
brain-segmentation.py
ge_scil_b0
median_otsu.png
siemens_scil_b0

README.md

Brain Segmentation


This example shows how to extract brain information and mask from an input b0 image using dipy, a diffusion imaging analysis package. This is based on an example available at dipy's gallery.

Original Experiment

The original experiment is composed by a single script named brain-segmentation.py, which consumes and segments the brain data that comes from a 1.5 tesla Siemens MRI (siemens_scil_b0).

To run this experiment without ReproZip, you will need to first install dipy.

ReproZip Package

The ReproZip package is available here (46.5 MB).

How to Reproduce

The experiment can be reproduced as follows:

$ reprounzip vagrant setup brain-segmentation.rpz brain-segmentation/
$ reprounzip vagrant run --enable-x11 brain-segmentation/

The output image with the results can be retrieved as follows:

$ reprounzip vagrant download brain-segmentation/ median_otsu.png

You can also perform the same prediction with an alternate input data (ge_scil_b0) as follows:

$ reprounzip vagrant upload brain-segmentation/ ge_scil_b0:siemens_scil_b0
$ reprounzip vagrant run --enable-x11 brain-segmentation/

And finally download the results as follows:

$ reprounzip vagrant download brain-segmentation/ median_otsu.png

Packing From Our Demo VM

If you are using our demo VM image, you can run the following:

$ vagrant ssh
$ cd reprozip-examples/brain-segmentation/
$ python brain-segmentation.py