How to convert MRI images into lmdb or hd5 format for caffe?

[sagar hukkire]

Hi All

I am doing image segmentation on MRI images with Caffe. I need to get the dicom imgaes into lmdb format?

Any script or guideline will be great help

[Patrick McNeil]

The easiest way would be to convert them to JPEG or PNG file.  Imagmagick is supposed to be able to read dicom and convert them to JPEG or PNG.

Patrick

[Evan Shelhamer]

Instead of converting to lmdb, it's most likely simpler to work directly from dicom while loading the data in Python. Here's an example Python data layer https://github.com/shelhamer/fcn.berkeleyvision.org/blob/master/voc_layers.py#L8-L116

If you have code to load your images and labels, you can adjust `load_image()` and `load_label()` accordingly.

Evan Shelhamer

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