kcho

#!/bin/bash

# 12th June 2020
# workshop by Usan Ong

# Environment settings
analysis_dir=${PWD}
trimmomatic=/Users/kevin/Downloads/Trimmomatic-0.39/trimmomatic-0.39.jar
hisat2=/Users/kevin/Downloads/hisat2-2.2.0/hisat2
#downloaded from hisat2 website

kcho

kcho

for i in $@
do
    echo ${i}
    MNIdir=${i}/DTI_MNI
    if [ ! -d ${MNIdir} ]
    then
        mkdir ${MNIdir}
    fi  

    # MNI registration

kcho

kcho

kcho

# Server
# BI server address
server=
id_at_server=

# Create id and append it to the BI server's authorized host list
ssh-keygen -t rsa
cat /root/.ssh/id_rsa.pub | ssh ${id_at_server}@${server} 'cat >> .ssh/authorized_keys'
#host checking
echo "Host *" >> /root/.ssh/config

kcho

import nibabel as nb
import numpy as np
from nilearn.image import resample_img
import pp
from glob import glob
import os
import re

def main():
    workshopDataLoc = '/media/workshop/openData_for_workshop/NITRC/workshop'

kcho

import nibabel as nb
import numpy.ma as ma
import numpy as np
from nilearn.image import resample_img
import pp
from glob import glob
import os
import re

def main():

kcho

import numpy as np
import cv2
from matplotlib import pyplot as plt






def drawMatches(img1, kp1, img2, kp2, matches):

kcho

import pandas as pd
import numpy
import os
import seaborn as sns
import nibabel as nib
import matplotlib
from nilearn import plotting, image
import nipype.interfaces.freesurfer as fs
import nipype.interfaces.fsl as fsl
from nipype import Node, MapNode, Workflow