pipitone

#!/bin/bash
filename=$1
datafile=$2

IFS=','    # splits rows by commas
while read ID symb chr start stop; do
  cat $datafile | awk "(\$2==$chr) && (\$3>=$start) && (\$3<=$stop) {print}"
done < $filename > PGC1_315immunegenetest.txt

pipitone

#!/bin/bash
#
# Edits a minc header, swapping occurances of two strings 
#
# (e.g. useful if you're trying to swap x/y dimension names)

minc=$1
attr1=$2
attr2=$3
tmpattr=att$RANDOM

pipitone

#!/usr/bin/env python
obj = open('surface.obj')
_, _, _, _, _, _, np = obj.readline().strip().split()
np = int(np)
vertices=[]
normals=[]
triangles=[]

# np vertices as (x,y,z)
min_x, min_y, min_z = 0, 0, 0

pipitone

#!/bin/bash
# 
# Monte Carlo Cross-Validation helper script
#
nfolds=$1
natlases=$2
ntemplates=$3
pool=(input/pool/brains/*.mnc)

function usage {

pipitone

Timestamp,Your Name:,Email address:,What is your career stage?,What is your discipline?,"In three sentences or less, please describe your current field of work or your research question.",What OS will you use on the laptop you bring to the workshop?,"With which programming languages, if any, could you write a program from scratch which imports some data and calculates mean and standard deviation of that data?",What best describes how often you currently program?,What best describes the complexity of your programming? (Choose all that apply.),A tab-delimited file has two columns showing the date and the highest temperature on that day. Write a program to produce a graph showing the average highest temperature for each month.,How familiar are you with Git version control?,"Consider this task: given the URL for a project on GitHub, check out a working copy of that project, add a file called notes.txt, and commit the change.",How familiar are you with unit testing and code coverage?,"Consider this task: given a 2

pipitone

Bhagwat-Brain
=============

To view the plots in this document, run the following: 

    module load R/3.0.2-precise64

From within R, run: 

    install.packages('knitr')

pipitone

---
- name: YP
  hosts: nis_slave:nis_client
  sudo: yes
  vars: 
    - min_uid: 1000
    - min_gid: 1000
    - nis_master: "{{groups['nis_master'][0]}}"
  tasks:
    # Basic idea here is we do things in two steps: 

pipitone

#! /usr/bin/perl
#
# autocrop - a program for extracting and manipulating the bounds of a
# MINC volume, with the capability to output parameters for mincresample
# or mincreshape, or a whole new (cropped) MINC volume.
#
# --------------------------------------------------------------------
# Copyright (c) 1994-96 Greg Ward, McConnell Brain Imaging Centre,
# Montreal Neurological Institute, McGill University.  Permission to
# use, copy, modify, and distribute this software and its

pipitone

#                                                                                                    
#                                                                                                    
#                                            ````````````                                            
#                                   ```.......................```                                    
#                              ```..................................``                               
#                           `...........................................``                           
#                        `.................................................``                        
#                     ``......................................................`                      
#                   `............................................................`                   
#                 `................................................................`                 

pipitone

#!/bin/bash
source /etc/profile.d/modules.sh
source /etc/profile.d/quarantine.sh
module load slicer/4.4.0
module load FSL/5.0.7 
module load DTIPrep/1.2.4
module load UKFTractography/2015-02-05

if [ -z "$4" ]; then
cat <<EOF