I’ve spent a little time with Caffe over the holiday break to try and understand how it might work in the context of real-time visualization/object recognition in more natural scenes/videos. Right now, I’ve implemented the following Deep Convolution Networks using the 1280×720 resolution webcamera on my 2014 Macbook Pro:

• VGG ILSVRC 2014 (16 Layers): 1000 ImageNet Object Categories (~ 7 FPS)
• VGG ILSVRC 2014 (19 Layers): 1000 Object Categories (~5 FPS)
• BVLC GoogLeNet: 1000 Object Categories (~ 24 FPS)
• Region-CNN ILSVRC 2013: 200 Object Categories (~ 22 FPS)
• BVLC Reference CaffeNet: 1000 Object Categories (~ 18 FPS)
• BVLC Reference CaffeNet (Fully Convolutional) 8×8: 1000 Object Categories (~12 FPS)
• BVLC Reference CaffeNet (Fully Convolutional) 34×17: 1000 Object Categories (~1 FPS)
• MIT Places-CNN Hybrid (Places + ImageNet): 971 Object Categories + 200 Scene Categories = 1171 Categories (~ 12 FPS)

The above image depicts the output from an 8×8 grid detection showing brighter regions as higher probabilities of the class “snorkel” (automatically selected by the network from 1000 possible classes as the highest probability).

So far I have spent some time understanding how Caffe keeps each layer’s data during a forward/backward pass, and how the deeper layers could be “visualized” in a … Continue reading...

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Destrieux atlas: aparc.a2009s
Desikan-Killiany atlas: aparc
Mindboggle: aparc.DKTatlas40
Brodman areas: BA and BA.thresh

We’ll first use freesurfer’s recon-all tool to perform a cortical reconstruction of our anatomical scans. Download freesurfer and register your copy. You’ll be sent an e-mail with a license. Follow the instructions and create the license file “.license” inside your freesurfer home directory (check the environment variable, FREESURFER_HOME, e.g., “$ echo $FREESURFER_HOME"). Then run the script, “$FREESURFER_HOME/FreeSurferEnv.sh” to setup necessary paths.

Next make sure you have set the environment variable for SUBJECTS_DIR to where you’d like your analysis to go (e.g., “$ export SUBJECTS_DIR=/some/directory“). For our example, we’ll keep this to a directory called “freesurfer” in our home directory, “~/”. Each subject we analyze will have its own folder insider … Continue reading...

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