代写PSYCH 727、代写MATLAB设计程序

日期：2023-04-26 08:57

LAB 1 (S1, 2023)

OUTLINE FOR THIS LAB

The purpose of this laboratory session is to familiarise you with the Linux

environment and the shell, MATLAB, and the data we are working with (fMRI

images).

Today we will cover:

1. Setting Up Remote Access to the Lab VM

2. Linux file structure

3. Introduction to Linux and the Shell

4. Introduction to MATLAB

5. Introduction to MRI data

1. SETTING UP REMOTE ACCESS TO THE LAB VM

To begin, we have to access the Virtual Machine (VM) we have set up for storing and analysing

data in this course. To do so, follow these steps:

Open x2go

Enter the following settings for your session

o Host = fospsychprd01.its.auckland.ac.nz

o Session type = XFCE

Log into your session with your UoA password

2

Open a Terminal Window (look for the computer screen icon at the top of your VM

session)

2. LINUX FILE STRUCTURE

/ (root)

bin course home

rrob042 jblo001

At the top of the file structure in Linux is the root directory that holds everything else. We refer

to it using a slash character / on its own; this is the leading slash in for instance the following

path: /home/rrob042.

The home directory path looks different on different operating systems. On Linux it looks like

e.g. /home/rrob042, whereas on Windows it would be C:\Users\rrob042. When you start

the shell, you are in your home directory by default, but for this course we will actually not

work in our home directories (we will work in /course, see below).

Inside the root directory are several other directories, such as bin, which is where some built-

in programs are stored. We have created another directory called course to store all course

materials.

/

(root)

bin course home

Data Software UserFolders

3

$

$ whoami

rrob042

dadd001 rrob042

In course there are several folders: Data, install, Software, and UserFolders. Inside

UserFolders you will find a directory that is named after your UPI; this is the directory in which

you will be working during this course. So instead of e.g. /home/rrob042 we will be working

in /course/UserFolders/rrob042.

3. INTRODUCTION TO THE LINUX SHELL

Linux is an open source operating system that was developed in the mid-1990s. It is a

powerful tool as you can do complex things with a few keystrokes. It is very useful for

neuroimaging where we have thousands of files per participant (e.g., you can rename all files

with one command).

The “shell” (also known as “bash”) is the way in which the user communicates with the

computer. We type commands into the shell, the shell “translates” these commands and orders

the computer to execute the command (usually to run a programme or “script”). It is called a

“shell” because it encases the complexities of the operating system so it is easier to interact

with.

Basic Shell Commands: Navigation

The part of the operating system responsible for managing files and directories is called the

file system. It organizes our data into files, which hold information, and directories (also

called “folders”), which hold files or other directories.

Several commands are used to create, inspect, rename, and delete files and directories.

To start exploring them, we will use a shell window:

The dollar sign (or another character) is a prompt, which shows us that the shell is waiting

for input; your shell may also add information (e.g., your user name) before the prompt. When

typing in commands listed here, do not type the prompt, only the commands that follow it.

Type the command whoami, then press the Enter key to send the command to the shell. The

command’s output is the ID of the current user, i.e., it shows us who the shell thinks we are:

When we type whoami, the shell:

finds a program called whoami,

runs that program,

displays that program’s output, then

displays a new prompt to tell us that it’s ready for more commands.

4

$ pwd

/Users/rrob042

$ ls

Desktop media

$ cd Desktop

$ cd rrob042

-bash: cd: rrob042: No such file or directory

$ cd ..

$ pwd

/Users/rrob042

Next, let’s find out where we are by running a command called pwd (which stands for “print

working directory”). At the moment, our current working directory is our default directory, i.e.,

the home directory. Here, the computer’s response is /Users/rrob042, which is my home

directory:

Now let’s learn the command that will let us see the contents of our own filesystem. We can

see what’s in our home directory by running ls, which stands for “listing”:

Now we can change our location to a different directory, so we are no longer located in our

home directory. The command to change locations is cd followed by a directory name to

change our working directory. cd stands for “change directory”, which is a bit misleading:

the command doesn’t change the directory, it changes the shell’s idea of what directory we

are in.

Let’s say we want to move to the Desktop. We can use the following command to get there:

We now know how to go down the directory tree: how do we go up? We might try:

Why do we get this error? With our methods so far, cd can only see sub-directories inside your

current directory. There are different ways to see directories above your current location; we’ll

start with the simplest.

There is a shortcut in the shell to move up one directory level that looks like this:

As mentioned above, .. is a special directory name meaning “the directory containing this one”,

or more succinctly, the parent of the current directory. If we run run cd .. and then type pwd,

we’re back in /Users/rrob042:

So far, when specifying directory names we have been using relative paths. When you use a

relative path with a command like ls or cd, it tries to find that location from where we are,

rather than from the root (beginning) of the file system. However, it is possible to specify

the absolute path to a directory by including its entire path from the root directory, which is

indicated by a leading slash (see section 2). The leading / tells the computer to follow the path

5

$ cp -r /course/labs/Lab1 /course/UserFolders/UPI

from the root of the file system, so it always refers to exactly one directory, no matter where

we are when we run the command.

Now we will copy a directory for this lab into our won personal directories in

/course/UserFolders. This directory contains a single anatomical MRI image that we will be

using in this lab.

6

$ matlab

Current working directory

Workspace

(variable list)

Contents of

current directory

History of

commands

Command window

cd /course/UserFolders/UPI

spm fmri

INTRODUCTION TO MATLAB

To start MATLAB just type matlab into the shell:

In the Command Window or shell we can run and debug our code. You can use all the basic

shell commands from section 1 (cd, ls, etc.) in the MATLAB shell.

INTRODUCTION TO MRI DATA

Let’s explore some real brain data.

Running SPM

Make sure you are in the right directory (in this case, the directory containing anat.nii is

probably a good place, but it might the directory for the subject or the study):

Open SPM:

7

A note about image file types.

DICOM (Digital Imaging and Communications in Medicine) format. Raw data from the scanner;

must be converted to Analyze or nifti format for analysis.

Analyze format. Each image has two files: .hdr (header file containing metadata) and .img (the

actual image).

Nifti (Neuroimaging Informatics Technology Initiative) format. In this format, images can be

stored in the two file presentation (.hdr/.img) or a one file presentation (.nii). A critical advance over

Analyze format is that nifti files store the orientation of the image in an unambiguous manner.

Moreover, time can be included as a fourth dimension.

For more information, see https://brainder.org/2012/09/23/the-nifti-file-format/

8

A note about xyz coordinate systems.

xyz coordinates refer to the location of any given voxel (3D pixel) or element in the 3D image/matrix.

However, there are two types of “spaces” or coordinate systems when dealing with MRI images:

voxel space and world space (or mm space). Below is a 2D example of each coordinate system.

You will notice that all the values in voxel space are positive, while world space includes positive and

negative values (relative to the “origin” or the coordinate, 0 0 0).

Display

In the GUI (Graphics User Interface) for SPM, click

on ‘Display’, and select the ‘anat.nii’ file to view the

structural image. You should see the following

image:

Exercise:

Images are actually just 3D matrices of numbers: each value in the matrix corresponds to an

intensity value of a voxel in the brain.

If you click anywhere on the image, you will see that below the coordinates will update as well

as the intensity value. Using this knowledge, complete the following table:

Coordinates (world space) Intensity Value Observations

31 -19 -17

-32 -59 14

31 41 -46

-60 41 66

5 11 7

9

Linux Commands

Command Operation Performed Example

. Current location

.. Up 1 directory from current location

--help provides info about a certain command cd--help

cd Change directory cd spm/subject1

cd ../ Change directory one up cd ../subject2

pwd Present working directory

ls List contents of current directory

ls -l List contents with details of all files

ls | more List contents at a user specified rate

cp Copy file to another directory cp input_file new location

cp 001.img ../subject2

Copy but give another name cp input_file output_file

cp 001.img func.img

Copy file to another directory AND give it

another name

cp input_file new

location/output_file

cp 001.img ../subject2/func.img

cp -r Copy whole directory cp -r input_dir output_dir

cp -r subject2 subject2_backup

mv Move a file (can be used to rename file) mv input_file output_file

mv 001.img func.img

Move file to another directory (i.e. "Cut and

paste" file)

mv input_file new location

mv 001.img ../subject2

more View the contents of a file more timings.txt

rm Remove file (delete) rm 001.img

rm -r (or rmdir) Remove directory rm -r subject1

cat Create a file (e.g. a text file) cat file_name.txt

cat timings.txt

* Wildcard *.* = all files e.g. cp *.*

*.img = all files with img as

extension

subj* = all files starting with

string "subj"

top Lists current users and activity on server

df -k

Gives memory capacity remaining on your

dir

emacs Opens a text editing program

emacs *.txt

Opens a text editing program with a file

name

emacs file_name.txt

emacs Timing_Files.txt

^c Cancel

exit Exit

mkdir mkdir (in current location) mkdir new_dir_name

rename Renaming rename test subj1_test

Renaming multiple files if needed rename test subj1_test test*

More linux commands are available here: http://linuxcommand.org/