Brain Plots

####Currently only supports openfmri group-level analysis

####How to Use

• Install CIFTI version of nibabel (DISCLAIMER: best to make dedicated environment for this script at the moment)
• Clone repo (including 32k Atlas)
• Use commented command at the top to run windowless
• Specify options with the following flags:
• -d (required): path to group results (up to tasks)
• -t (required): tasks separated by spaces
• -o: path to output directory (default is current working directory)
• -a: path to 32k_ConteAtlas_v2 folder (default is current working directory)
• -i: flag to make uninflated brain output (default is inflated)
• -s: flag to make whole brain output (default is split)
• -ss: flag to remove quad split
• -th: set threshold (must be a float) (default is 2.3)
• -dt: set display threshold (int) (default is 6)

#####Sample Use om_py_plot_surfs.py -d /om/project/voice/processedData/groupAnalysis/may2016_model101/one_sample/model101 -t task001 task002 -ss -th 3.0 -dt 5

###TO-DO

1. Add mask input to show brain coverage
2. Mutable image size
3. Handle flexible directory structure - Subject Level QA, Group Analysis, Etc