Create a subject-specific Wang 2015 visual field atlas annotation.

make_wang_atlas_annot.py

""""Create a subject-specific Wang 2015 visual field atlas annotation.

Convert the Wang atlas in subject-space (as created by Noah Benson's
template mapping scripts) from segmentation format to annotation format.

"""
import os
import sys
import numpy as np
import matplotlib.pyplot as plt

if __name__ == "__main__":

    _, subj = sys.argv

    seg_temp = "../data/{}/surf/{}.wang2015_atlas.mgz"
    annot_temp = "../data/{}/label/{}.wang2015_atlas.annot"
    ctab_fname = "wang2015_atlas.ctab"

    names = ["Unknown",
             "V1v", "V1d", "V2v", "V2d", "V3v", "V3d",
             "hV4", "VO1", "VO2", "PHC1", "PHC2",
             "V3A", "V3B", "LO1", "LO2", "TO1", "TO2",
             "IPS0", "IPS1", "IPS2", "IPS3", "IPS4", "IPS5",
             "SPL1", "hFEF"]

    labels = np.arange(len(names))

    rgba = plt.cm.Spectral(np.linspace(0, 1, labels.size - 1))
    rgba = np.r_[[[0, 0, 0, 0]], rgba]
    rgba = (rgba * 255).astype(np.int)

    ctab = np.c_[labels, names, rgba]

    np.savetxt(ctab_fname, ctab, delimiter="\t", fmt="%s")

    for hemi in ["lh", "rh"]:

        cmdline = ["mris_seg2annot",
                   "--ctab", ctab_fname,
                   "--seg", seg_temp.format(subj, hemi),
                   "--o", annot_temp.format(subj, hemi),
                   "--h", hemi,
                   "--s", subj]

        os.system(" ".join(cmdline))