dgutman

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
<properties>
<comment>
	configuration file for DicomServer, by karchie@npg.wustl.edu
</comment>

<entry key="arcspec">/home/xnat/xnat_data/cache/archive_specification.xml</entry>
<entry key="xnat_url">http://localhost:8080/xnat</entry>
<entry key="user">admin</entry>

dgutman

## David A Gutman  dgutman _at_ emory.edu
## This script walks through install an XNAT Ubuntu Virtual Machine for a VMware Host 
## Note:  this script can not be run as a single bash script.
# This is a fork/update of johnpaulett's guest setup script
# https://gist.github.com/johnpaulett/206346

## VMWARE Setup:  I allocated 80GB for the main XNAT partition (using Thin Provisioning)
## Also I set up an additional disk as a standalone partition to actually store all my data
## Presumably you do not want to have your VM image with your database/XNAT/etc in the same VM as 
## storage

dgutman

import urllib2

import json
import os
import csv
import pandas as pd
import xlrd
from pandas.io.parsers import ExcelFile
from xml.dom import minidom

dgutman

import nipype
import os,glob,sys,shutil
sys.path.append("/usr/lib/ants/")
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
import nipype.interfaces.ants as ants
from nipype.interfaces.ants import Registration, RegistrationSynQuick,WarpImageMultiTransform
from nipype.interfaces.fsl import Info

dgutman

## This script is a nipype pipeline to combine two MRI images for the same subject that have been acquired in different orientations
## and different spatial resolution.  

__author__ = 'dgutman' 
"""" This script will take a very disorganized set of axial that had a mask manually drawn in the axial plain, as well as sagittal dog images  
and register and reorient them so the data can be used for later averaging

The mask doesn't have to be perfect, but should be fairly close and not include excessive 
amounts of neck

dgutman

exec sp_helpindex 'dbo.MF_EMR_SPECIALTESTSPROCEDURES'

 HealthFactorTypeSID
SELECT [DWViewSchema]
,[DWViewName]
,[DWPartitionKey]
,[DWPartitionKeyDataType]
FROM [CDWWork].[Meta].[DWView]
WHERE [DWViewName] = 'HealthFactor'
 is another way