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batch crop and color-correction

I have about 2400 NEF files taken from a stationary position of a stationary subject over about 3 days. Due to the change in lighting conditions there are blocks of files that are lighter or darker and with somewhat differing color. I need to crop and adjust the color so that the set of images is uniform so that I can upload them to a program (Amira) to process them into a 3-D model.

I've been trying to use David's Batch Processor (for Windows) with GIMP 2.6.8 but it was applying other unwanted changes to the images (such as lens correction). Now it's not even running a batch process on the files.

Does anyone know how I can get David's Batch Processor to only crop and adjust the colors so that the image set will be uniform, or another way to accomplish this task?

THANKS!

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