margulies

import h5py, sys, io, numpy as np
from mapalign import embed, dist, align
from sklearn.metrics import pairwise_distances
import scipy.io
from scipy.sparse.linalg import eigsh, eigs

num = '313'
hcp = h5py.File('/scr/animals1/hcp_RS_all/hcp.all.%s.rowise.all.mat' % num)

## For PCA: 

margulies

emat = scipy.io.loadmat('economo/ECONO_DATA_ORIG.mat')
labels = []
for x in emat['ECONOMO_regions'][0]:
    labels.append(x[0].encode('ascii'))
    
def read_economo():
    data = []
    header = []
    thresh = 100 # currently arbitrarily high, but could be used to remove data columns with excessive NaNs...
    for x in emat.keys():

margulies

import xml.etree.ElementTree as ET
import numpy as np
import pandas as pd
from colormap import rgb2hex

path_style = "stroke:#000000;stroke-width:0;stroke-opacity:0;fill-opacity:1;fill:"
SVG_NS = "http://www.w3.org/2000/svg"
             
def parse_xml(data): 
  '''

margulies

<div>
    <a href="https://plot.ly/~margulies/14" target="_blank" title="" style="display: block; text-align: center;"><img src="https://plot.ly/~margulies/14.png" alt="" style="max-width: 100%;width: 600px;"  width="600" onerror="this.onerror=null;this.src='https://plot.ly/404.png';" /></a>
    <script data-plotly="margulies:14"  src="https://plot.ly/embed.js" async></script>
</div>

margulies

# changes are in lines with "if mask is not None:"
# "lenient" allows more liberal inclusion for specific cases where needed
# "label" uses median instead of mean to get values (for labels)

def plot_surf_stat_map(coords, faces, stat_map=None,
        elev=0, azim=0,
        cmap='jet',
        threshold=None, bg_map=None,
        mask=None,
        bg_on_stat=False,

margulies

%matplotlib inline

from PIL import Image

i1 = Image.open('smith_dist_plot.png')
i2 = Image.open('smith_brains.png')
# print np.shape(i1)
# print np.shape(i2)

result = Image.new("RGBA", (np.shape(i1)[1]+50, np.shape(i1)[0]))

margulies

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<!-- Generated by: TmTheme-Editor                 -->
<!-- ============================================ -->
<!-- app:  http://tmtheme-editor.herokuapp.com    -->
<!-- code: https://github.com/aziz/tmTheme-Editor -->
<plist version="1.0">
<dict>
	<key>name</key>
	<string>neuro</string>

margulies

# -*- coding: utf-8 -*-
"""
Created on Tue Apr  7 11:49:45 2015

@author: jgolchert
"""
#Run in terminal before staring script
#export AFNI_1D_ZERO_TEXT=YES

import os                                    # system functions\n",

margulies

function[] = distance_connectivity_calc()

topPercent=0.1;

surf = SurfStatReadSurf('surf_lh_fs.mgh.obj');
conn = data(1:length(surf.coord),:);

cortex = load('lh.cortex.1D.txt');
cortex = cortex(:,1)+1;
noncortex = ones([1 length(surf.coord)]);

margulies

#!/bin/bash

3dSetupGroupInCorr -LRpairs surf_lh_fs.asc surf_rh_fs.asc -prefix group.all \
  test_surface_extract/surfaceData_h004_935_lh.niml.dset test_surface_extract/surfaceData_h004_935_rh.niml.dset \
  test_surface_extract/surfaceData_w353_935_lh.niml.dset test_surface_extract/surfaceData_w353_935_rh.niml.dset 
  
# Then run:  

# suma -spec surf_asc.spec -niml &
# 3dGroupInCorr -setA group.all.grpincorr.niml -suma