1. Introduction to Unix for FreeSurfer Users

2. What is Unix/Linux? An operating system (like Windows and OS X)
Linux is the free, modifiable, and redistributable version of Unix
Why use it?

3. What is Unix/Linux? An operating system (like Windows and OS X)
Linux is the free, modifiable, and redistributable version of Unix
Why use it?
power to write many scripts with many commands to work with lots of data
to use computer resources on the network efficiently, such as clusters

4. Getting Started For course-provided Linux computers:
Communicate with operating system through a “shell” or terminal window.
For course-provided Linux computers:
Double click Terminal icon on Desktop
For Macs:
Applications > Utilities > XQuartz (double click)
Applications > Utilities > Terminal

5. Linux Desktop

6. Directories (think folders in Windows)
Unix uses a hierarchical file system
(think folders in Windows)

7. Directories (think folders in Windows)
Unix uses a hierarchical file system
(think folders in Windows)
Home is like “My Computer”

8. Directories (think folders in Windows)
Unix uses a hierarchical file system
(think folders in Windows)
Home is like “My Computer”
Like “My Documents”

9. Directories
Unix uses a hierarchical file system (think folders in Windows)
Home is like “My Computer”
Like “My Documents”
Like “My Photos”

10. Directories
Unix uses a hierarchical file system (think folders in Windows)
Home is like “My Computer”
Like “My Documents”
Like “My Photos”
picture.jpg

11. command -option1 –option2 file
Anatomy of a Command
command -option1 –option2 file
command - -help

12. command -option1 –option2 file
Anatomy of a Command
command -option1 –option2 file
command help
Try:
ls --help

13. shows “present working directory” or current location as a path
Type:
and hit enter. Should see
shows “present working directory” or current location as a path
/Users/YourName OR
pwd
/home/nmrclass

14. Navigating Directories
“change directory”: move into a folder “list”: see contents of directory
cd __ ls
ls __

15. Navigating Directories
“change directory”: move into a folder “list”: see contents of directory
cd __ ls
ls __
Desktop matlab tmp TUTORIAL_DATA

16. Directory Contents
List contents of directory you are in lists names of directories/files ls
ls -a
ls -l
ls -lrt

17. Directory Contents
List contents of directory you are in lists names of directories/files lists hidden files too ls
ls -a
ls -l
ls -lrt
.cshrc
.bashrc
.alias

18. Directory Contents
List contents of directory you are in lists names of directories/files lists hidden files too lists file details drwxrwx--- ls
ls -a
ls -l
ls -lrt
user
group
others

19. Directory Contents
List contents of directory you are in lists names of directories/files lists hidden files too lists file details lists recent files last ls
ls -a
ls -l
ls -lrt

20. Save Some Time
Filename Completion hit Tab key should see hit enter History hit key should see
ls Des
ls Desktop
ls Desktop

21. /home/nmrclass/practice
Changing Directories
makes a new directory “practice” changes to directory “practice”
mkdir practice
ls -lrt
/home/nmrclass
pwd
should see
cd practice
pwd
/home/nmrclass/practice
should see ls
should see
Nothing!

22. Changing Directories

23. Changing Directories makes folder “stuff” inside practice
mkdir stuff
makes folder “stuff” inside practice ls
should see “stuff”

24. /home/nmrclass/practice/stuff
Changing Directories
shows one directory up
ls ..
can also do (but don’t right now):
cd ..
cd ../..
ls ../..
goes up two!
pwd
/home/nmrclass/practice/stuff
should see

25. Format > Make plain text
Using an Editor
emacs mynotes.txt
open -e mynotes.txt
If using a Mac:
Type: I could write a script.
File > Save (Buffer)
File > Exit emacs
should see “mynotes.txt”
Format > Make plain text
File > Save ls

26. Format > Make plain text
Using an Editor
gedit mynotes.txt
open -e mynotes.txt
If using a Mac:
Type: I could write a script.
File > Save (Buffer)
File > Exit emacs
should see “mynotes.txt”
Format > Make plain text
File > Save ls

27. Using an Editor

28. Copying files is the copy command learn all the options or “arguments”cp
cp --help
learn all the options or “arguments”
cp mynotes.txt stuff
cd stuff ls
more mynotes.txt

29. Copying files is the copy command learn all the options or “arguments”cp
cp --help
learn all the options or “arguments”
cp mynotes.txt stuff
cd stuff ls
less mynotes.txt

30. Copying / Moving files Could also use do:
cp mynotes.txt myothernotes.txt
mv myothernotes.txt hernotes.txt
mv hernotes.txt

31. Removing Files
pwd
should be in “stuff” ls
rm mynotes.txt ls

32. Things to know Case sensitive Does not like spaces in file names
(e.g. filename.txt vs. file name.txt)
Ctrl+c kills a process & brings back command prompt
Type ‘q’ to quit the program ‘less’
Highlight & middle click to copy & paste
Use ‘&’ to open a program in the background
Cannot open a 2nd program if do not have a command prompt

33. Review
no double clicking mkdir ls cd pwd emacs, gedit, vi, pico cp rm

34. Using FreeSurfer tell Operating System where FreeSurfer is
With FreeSurfer, certain variables must be set in order to use it correctly: FREESURFER_HOME SUBJECTS_DIR
tell Operating System where FreeSurfer is
tell FreeSurfer where data is

35. To use FreeSurfer you’ll have to do:
Required Variables
To use FreeSurfer you’ll have to do:
setenv FREESURFER_HOME /home/apps/freesurfer
tell Operating System where FreeSurfer is
source $FREESURFER_HOME/SetUpFreeSurfer.csh
source this script to get your computer ready to use FreeSurfer (sources other scripts & sets other variables)
setenv SUBJECTS_DIR /path/to/data

36. To use FreeSurfer you’ll have to do:
Required Variables
To use FreeSurfer you’ll have to do:
export FREESURFER_HOME=/home/apps/freesurfer
tell Operating System where FreeSurfer is
source $FREESURFER_HOME/SetUpFreeSurfer.csh
source this script to get your computer ready to use FreeSurfer (sources other scripts & sets other variables)
export SUBJECTS_DIR=/path/to/data

37. setenv SUBJECTS_DIR /path/to/data
Required Variables
To go to location of your data: $ means take the value of the variable
setenv SUBJECTS_DIR /path/to/data
cd $SUBJECTS_DIR

38. setenv SUBJECTS_DIR /path/to/data
Required Variables
To go to location of your data: $ means take the value of the variable
setenv SUBJECTS_DIR /path/to/data
cd $SUBJECTS_DIR
aka
cd /path/to/data

39. setenv TEST_VARIABLE yourname$
How ‘echo’ works: To set a variable: To check what a variable is set to:
echo anything
setenv TEST_VARIABLE yourname
echo $TEST_VARIABLE

40. echo $FREESURFER_HOME
Required Variables
With FreeSurfer, certain variables must be set in order to use it correctly: FREESURFER_HOME SUBJECTS_DIR
tell Operating System where FreeSurfer is
tell FreeSurfer where data is
To check variables
echo $FREESURFER_HOME
echo $SUBJECTS_DIR

41. More Help
LineNavigation Homework packet Links on Wiki under “Unix Tutorial” Glossary of Unix commands

42. The End
Good Luck!