Unix Tutorial for FreeSurfer Users Allison Stevens.
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Unix Tutorial for
FreeSurfer Users
Allison Stevens
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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?
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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
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Getting Started
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
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Warm Up
Type: and hit enter.
date
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Warm Up
Type: and hit enter. Should see
date Mon Apr 6 8:05:24 EDT 2009
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Warm Up
Type: and hit enter. Should see
Type: and hit enter.
date Mon Apr 6 8:05:24 EDT 2009
cal
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Warm Up
Type: and hit enter. Should see
Type: and hit enter. Should see
date Mon Apr 6 8:05:24 EDT 2009
cal April 2009Su Mo Tu We Th Fr Sa 1 2 3 4 5 6 7 8 9 10 1112 13 14 15 16 17 1819 20 21 22 23 24 2526 27 28 29 30
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Directories
• Unix uses a hierarchical file system (think folders in Windows)
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Directories
• Unix uses a hierarchical file system (think folders in Windows)
Home is like “My Computer”
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Directories
• Unix uses a hierarchical file system(think folders in Windows)
Home is like “My Computer”
Like “My Documents”
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Directories
• Unix uses a hierarchical file system (think folders in Windows) Home is like
“My Computer”
Like “My Documents”
Like “My Photos”
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Directories
• Unix uses a hierarchical file system (think folders in Windows) Home is like
“My Computer”
Like “My Documents”
Like “My Photos”
picture.jpg
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Location
path:/MyComputer/MyDocuments/MyPhotos
Type: and hit enter. Should see
shows “present working directory” or current location as a path
pwd
/home/nmrclass
/Users/YourName
OR
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Opening a Directory
• Not double clicking • Type command to “open”
• Commands to open files will differ
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Navigating Directories
“change directory”: move into a folder
“list”: see contents of directory
ls
cd __
ls __
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Navigating Directories
“change directory”: move into a folder
“list”: see contents of directory
ls
cd __
ls __
Desktop matlab tmp TUTORIAL_DATA
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Anatomy of a Command
command -option1 –option2 file
command - -help
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Anatomy of a Command
command -option1 –option2 file
command - -help
ls --help
Try:
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Directory Contents
• List contents of directory you are in lists names of directories/filesls
ls -lrt
ls -l
ls -a
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Directory Contents
• List contents of directory you are in lists names of directories/files lists hidden files too
.cshrc
.bashrc
.alias
ls
ls -lrt
ls -l
ls -a
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Directory Contents
• List contents of directory you are in lists names of directories/files lists hidden files too lists file details
drwxrwx---
user groupothers
ls
ls -lrt
ls -l
ls -a
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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 -lrt
ls -l
ls -a
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Save Some Time
Filename Completion
hit Tab key should see hit
enter
History
hit key should see
ls Des
ls Desktop
ls Desktop
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Changing Directories
makes a new directory “practice”
changes to directory “practice”
mkdir practice
cd practice
ls -lrt
pwd
ls
pwd
/home/nmrclass
/home/nmrclass/practice
should see
should see
should see Nothing!
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Changing Directories
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Changing Directoriesmkdir stuff
ls
makes folder “stuff” inside practiceshould see “stuff”
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Using an Editor
If using a Mac:
Type: I could write a script.File > Save (Buffer)
File > Exit emacs
should see “mynotes.txt”
emacs mynotes.txt open -e mynotes.txt
ls
Format > Make plain textFile > Save
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Using an Editor
If using a Mac:
Type: I could write a script.File > Save (Buffer)
File > Exit emacs
should see “mynotes.txt”
gedit mynotes.txt
ls
Format > Make plain textFile > Save
open -e mynotes.txt
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Using an Editor
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Copying files
ls
cp --help
cp mynotes.txt stuff
cd stuff
more mynotes.txt
learn all the options or “arguments”
is the copy command
cp
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Copying files
ls
cp --help
cp mynotes.txt stuff
cd stuff
less mynotes.txt
learn all the options or “arguments”
is the copy command
cp
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Changing Directories
shows one directory up
ls ..
pwd /home/nmrclass/practice/stuff
ls ../.. goes up two!cd ..
should see
cd ../..
can also do (but don’t right now):on
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Copying / Moving files
cp mynotes.txt myothernotes.txt
Could also use do:
mv myothernotes.txt hernotes.txt
mv hernotes.txt ..
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Removing Files
rm mynotes.txt
ls
pwd should be in “stuff”
ls
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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
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Review
• no double clicking• mkdir• ls• cd• pwd• emacs, gedit, vi, pico• cp• rm
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Using FreeSurfer
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
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Required Variables
• To use FreeSurfer you’ll have to do:
setenv FREESURFER_HOME /home/apps/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
tell Operating System where FreeSurfer is
source this script to get your computer ready to use FreeSurfer (sources other scripts & sets other variables)
setenv SUBJECTS_DIR /path/to/data
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Required Variables
• To use FreeSurfer you’ll have to do:
export FREESURFER_HOME=/home/apps/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
tell Operating System where FreeSurfer is
source this script to get your computer ready to use FreeSurfer (sources other scripts & sets other variables)
export SUBJECTS_DIR=/path/to/data
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Required Variables
To go to location of your data:
$ means take the value of the variable
cd $SUBJECTS_DIR
setenv SUBJECTS_DIR /path/to/data
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Required Variables
To go to location of your data:
$ means take the value of the variable
cd $SUBJECTS_DIRaka
cd /path/to/data
setenv SUBJECTS_DIR /path/to/data
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$
How ‘echo’ works:
To set a variable:
To check what a variable is set to:echo $TEST_VARIABLE
setenv TEST_VARIABLE yourfirstname
echo Allison is cool.
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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
echo $FREESURFER_HOME
echo $SUBJECTS_DIR
To check variables
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More Help
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/CommandLineNavigation
Links on Wiki under “Unix Tutorial”
Glossary of Unix commands
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The End
Good Luck!
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Intro to FreeSurfer Jargon
voxelsurfacevolumevertexsurface-basedreconcortical, subcorticalparcellation/segmentationregistration, morph, deform, transforms
(computing vs. resampling)
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What FreeSurfer Does…
FreeSurfer creates computerized models of the
brain from MRI data.
Input:T1-weighted (MPRAGE)
1mm3 resolution(.dcm)
Output:Segmented & parcellated conformed
volume(.mgz)
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Intro to FreeSurfer Jargon
voxel
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Intro to FreeSurfer Jargon
surface
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Intro to FreeSurfer Jargon
surface
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Intro to FreeSurfer Jargon
vertex
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Recon
“recon your data”…short for reconstruction
…cortical surface reconstruction…shows up in command
recon-all
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Recon
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Volumes
orig.mgz T1.mgz brainmask.mgz wm.mgz filled.mgz(Subcortical Mass)
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Cortical vs. Subcortical GM
coronal
sagittal
subcortical gm
cortical gm
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Cortical vs. Subcortical GM
coronal
sagittal
subcortical gm
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Parcellation vs. Segmentation
(subcortical) segmentation
(cortical) parcellation
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Intro to FreeSurfer Jargon
voxelsurfacevolumevertexsurface-basedreconcortical, subcorticalparcellation/segmentationregistration, morph, deform, transforms
(computing vs. resampling)
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FreeSurfer Questions
Search for terms and answers to all your questions in the Glossary,
FAQ, orFreeSurfer Mailing List Archives
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Registration
Goal:to find a common coordinate system for the input data sets
Examples: • comparing different MRI images of the
same individual (longitudinal scans, diffusion vs functional scans)
• comparing MRI images of different individuals
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12/13/2011Flirt 6 DOF
subject
Flirt 9 DOF
target
Inter-subject, uni-modal example
Flirt 12 DOF
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Linear registration: 6, 9, 12 DOF
Flirt 6 DOFFlirt 9 DOFFlirt 12 DOFsubjecttarget
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Linear registration: 6, 9, 12 DOF
targetsubjectFlirt 6dofFlirt 9dofFlirt 12 DOF
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Linear registration: 6, 9, 12 DOF
targetsubjectFlirt 6 DOFFlirt 9 DOFFlirt 12 DOF
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Intra-subject, multi-modal example
before spatial alignment
after spatial alignment
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before spatial alignment
after spatial alignment
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before spatial alignment
after spatial alignment
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Inter-subject non-linear example
target CVS reg
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Some registration vocabulary
• Input datasets:– Fixed / template / target– Moving / subject
• Transformation models– rigid– affine– nonlinear
• Objective / similarity functions
• Applying the results– deform, morph, resample, transform
• Interpolation types– (tri)linear– nearest neighbor
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Writing Scripts
• Putting multiple commands together. • Automatically running a sequence of
commands• Example: create a file named
my_first_script.csh with the contents: #!/bin/csh
setenv name FreeSurferecho I love $name !
% chmod u+x my_first_script.csh% ./my_first_script.csh
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Loops in Scripts
• You can create loops, if statements, …• Example: create a file named
my_first_loop.csh with the contents:
#!/bin/csh
foreach name (‘Bill Murray’ ‘Wes Anderson’)echo I love $name !
end
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Inputs to Scripts
• You can create take inputs from the command line
• Example: create a file named my_first_IO.csh with the contents:
#!/bin/csh
echo The $0 command is called with $#argv parametersecho parameter 1 is $1echo parameter 2 is $2
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Required Variables
• To use FreeSurfer you’ll have to do:
setenv FREESURFER_HOME /home/apps/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
tell Operating System where FreeSurfer is
source this script to get your computer ready to use FreeSurfer (sources other scripts & sets other variables)
setenv SUBJECTS_DIR /path/to/data
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Registration
-align subjects-common space-reference points b/w subjects will be
sametransforms
template
deform
morph
warp
compute
resample
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alias e emacsman alias
ls file* lists file1, file2, file3ls file[12] lists file1 and file2 but not file3
command >>& file.txt save output to screen and errors in text file