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 fileAnatomy of a Command command -option1 –option2 file command - -help

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

13 shows “present working directory” or current location as a pathType: 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/practiceChanging 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 practicemkdir stuff makes folder “stuff” inside practice ls should see “stuff”

24 /home/nmrclass/practice/stuffChanging 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 textUsing 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 textUsing 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 isWith 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/dataRequired 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/dataRequired 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_HOMERequired 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!