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Unix Tutorial for Freesurfer Users

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Unix Tutorial for Freesurfer Users What is Unix/Linux? • An operating system Unix Tutorial (like Windows and OS X) for • Linux is the free, modifiable, and FreeSurfer Users redistributable version of Unix Allison Stevens •Why use it? What is Unix/Linux? Getting Started • An operating system Communicate with operating system (like Windows and OS X) through a “shell” or terminal window. • Linux is the free, modifiable, and For Linux: redistributable version of Unix Double click Terminal icon on Desktop •Why use it? For Macs: – power to write many scripts with many Double click on hard drive commands to work with lots of data Applications > Utilities > X11 (double click) 1 Warm Up Warm Up Type: Type: date and hit enter. date and hit enter. Should see Mon Apr 6 8:05:24 EDT 2009 Warm Up Warm Up Type: Type: date and hit enter. Should see Mon Apr 6 8:05:24 EDT 2009 date and hit enter. Should see Mon Apr 6 8:05:24 EDT 2009 Type: Type: April 2009 cal and hit enter. cal and hit enter. Should see Su Mo Tu We Th Fr Sa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 2 Directories Directories • Unix uses a hierarchical file system • Unix uses a hierarchical file system (think (think folders in Windows) folders in Windows) Home is like “My Computer” Directories Directories • Unix uses a hierarchical file system (think • Unix uses a hierarchical file system (think folders in Windows) folders in Windows) Home is like Home is like “My Computer” “My Computer” Like “My Like “My Documents” Documents” Like “My Photos” 3 Directories Opening a Directory • Unix uses a hierarchical file system (think • There is no “double click” folders in Windows) • Must enter command for Home is like “My Computer” “double click” aka “open” at the command prompt Like “My Documents” Like “My Photos” picture.jpg • Different command for “open” depending on file, program Location Directories Type: /home/nmrclass • Unix uses a hierarchical file system (think and hit enter. Should see OR folders in Windows) pwd Home is like /Users/YourName “My Computer” Like “My shows “present working directory” or current Documents” location as a path Like “My similar to: Photos” /MyComputer/MyDocuments/MyPhotos picture.jpg 4 Navigating Directories Navigating Directories cd __ “change directory”: move into a folder cd __ “change directory”: move into a folder ls ls “list”: see contents of directory “list”: see contents of directory ls __ ls __ Desktop multimodal_poster2.ppt subjects tmp matlab oct08 surfer.log vrfp-savoy-techs Save Some Time Anatomy of a Command Filename Completion ls Des hit Tab key command -argument1 –argument2 file should seels Desktop hit enter History command --help hit key should see ls Desktop 5 Anatomy of a Command Directory Contents • List contents of directory you are in ls lists names of directories/files ls -a command -argument1 –argument2 file ls -l ls -lrt command --help Try: ls --help Directory Contents Directory Contents • List contents of directory you are in • List contents of directory you are in ls lists names of directories/files ls lists names of directories/files ls -a lists hidden files too ls -a lists hidden files too ls -l ls -l lists file details ls -lrt ls -lrt drwxrwx--- .xdebug_tkmedit .cshrc .alias user group others 6 Directory Contents Changing Directories • List contents of directory you are in mkdir practice makes a new directory “practice” ls lists names of directories/files ls OR ls -lrt ls -a lists hidden files too pwd should see /home/nmrclass ls -l lists file details ls -lrt lists recent files last cd practice changes to directory “practice” pwd should see /home/nmrclass/practice ls should see Nothing! Changing Directories Changing Directories mkdir stuff makes folder “stuff” inside practice ls should see “stuff” cd stuff change to directory “stuff” ls pwd should see /home/nmrclass/practice/stuff 7 Changing Directories Using an Editor emacs mynotes.txt If using a Mac: pico mynotes.txt Type: I could write a script in here. File > Save (Buffer) Ctrl-x if using pico and then ‘Y’ and enter can also do: ls .. shows one directory up File > Exit emacs cd .. cd ../.. ls ls ../.. goes up two! should see “mynotes.txt” pwd should see /home/nmrclass/practice Using an Editor Copying files cp is the copy command cp --help learn all the options or “arguments” cp mynotes.txt stuff/ cd stuff ls more mynotes.txt 8 Copying files Copying / Moving files cp is the copy command Could also use do: cp --help learn all the options or “arguments” cp mynotes.txt myothernotes.txt cp mynotes.txt stuff/ mv mynotes.txt myothernotes.txt cd stuff mv mynotes.txt stuff/ ls less mynotes.txt Removing Files Removing Files pwd should be in “stuff” pwd should be in “stuff” ls ls rm mynotes.txt rm mynotes.txt ls ls cd .. goes to “practice” cd .. goes to “practice” ls ls rmdir stuff rmdir stuff ls ls rm mynotes.txt rm mynotes.txt 9 Removing Files Removing Files pwd should be in “stuff” pwd should be in “practice” ls cd .. goes to “Home” rm mynotes.txt rmdir practice ls cd .. goes to “practice” ls ls rmdir stuff ls rm mynotes.txt Review Using FreeSurfer • no double clicking With FreeSurfer, certain variables must be • make a directory set in order to use it correctly: • list contents of directory FREESURFER_HOME • go in and out of a directory and determine tell Operating System where FreeSurfer is current location • make a text file SUBJECTS_DIR • copy files tell FreeSurfer where data is • remove files and directories 10 Required Variables Required Variables • To use FreeSurfer you’ll have to do: setenv SUBJECTS_DIR /path/to/data setenv FREESURFER_HOME /home/apps/freesurfer To go to location of your data: tell Operating System where FreeSurfer is cd $SUBJECTS_DIR source $FREESURFER_HOME/SetUpFreeSurfer.csh source this script to get your computer $ means take the value of the variable ready to use FreeSurfer (sources other scripts & sets other variables) setenv SUBJECTS_DIR /path/to/data Required Variables $ setenv SUBJECTS_DIR /path/to/data To set a variable: setenv TEST_VARIABLE yourfirstname To go to location of your data: How ‘echo’ works: cd $SUBJECTS_DIR aka echo Allison is cool. cd /path/to/data $ means take the value of the variable To check what a variable is set to: echo $TEST_VARIABLE 11 Visualization Tools More Help • For FreeSurfer visualization tools: http://surfer.nmr.mgh.harvard.edu/fswiki /FsTutorial/CommandLineNavigation tkmedit subj001 T1.mgz -aux wm.mgz tksurfer subj001 lh inflated Links on Wiki under “Unix Tutorial” VisualizationTool subject data_file -aux other_data_file Glossary of Unix commands VisualizationTool subject hemisphere data_file The End Good Luck! 12.
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