Transcript Unix Tutorial for FreeSurfer Users

Unix Tutorial
for
FreeSurfer Users
Ani Varjabedian
Helpful To Know
• Freesurfer Tutorial Wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
• Questions?
• Answers:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
/QuestionAnswers
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?
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?
– Freedom to modify and customize
– power to write many scripts with
multiple commands to manage data
– to use computer resources on the network
efficiently, such as clusters
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
Warm Up
Type:
date
and hit enter.
Warm Up
Type:
date
and hit enter. Should see
Mon Apr 6 8:05:24 EDT 2009
Warm Up
Type:
date
and hit enter. Should see
Type:
cal
and hit enter.
Mon Apr 6 8:05:24 EDT 2009
Warm Up
Type:
date
and hit enter. Should see
Mon Apr 6 8:05:24 EDT 2009
Type:
cal
and hit enter. Should see
April 2009
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
Directories
• Unix uses a hierarchical file system
(think folders in Windows)
Directories
• Unix uses a hierarchical file system
(think folders in Windows)
Home is like
“My Computer”
Directories
• Unix uses a hierarchical file system
(think folders in Windows)
Home is like
“My Computer”
Like “My
Documents”
Directories
• Unix uses a hierarchical file system
(think folders in Windows)
Home is like
“My Computer”
Like “My
Documents”
Like “My
Photos”
Directories
• Unix uses a hierarchical file system
(think folders in Windows)
Home is like
“My Computer”
Like “My
Documents”
Like “My
Photos”
picture.jpg
Location
path:
/MyComputer/MyDocuments/MyPhotos
Type:
pwd
/home/nmrclass
and hit enter. Should see
OR
/Users/YourName
shows “present working directory” or current
location as a path
Opening a Directory
• Not double clicking
• Type command to “open”
• Commands to open files will differ
Navigating Directories
cd __
“change directory”: move into a folder
ls
ls __
“list”: see contents of directory
Navigating Directories
cd __
“change directory”: move into a folder
ls
ls __
“list”: see contents of directory
Desktop matlab tmp TUTORIAL_DATA
Anatomy of a Command
command -option1 –option2
command - -help
For Mac:
man __
file
Anatomy of a Command
command -option1 –option2
command
file
- -help
Try:
ls --help
or
man ls
Directory Contents
• List contents of directory you are in
ls
ls -a
ls -l
ls -lrt
lists names of directories/files
Directory Contents
• List contents of directory you are in
ls
ls -a
lists names of directories/files
lists hidden files too
ls -l
ls -lrt
.cshrc
.bashrc
.alias
Directory Contents
• List contents of directory you are in
ls
ls -a
ls -l
lists names of directories/files
lists hidden files too
lists file details
ls -lrt
drwxrwx--user group
others
Directory Contents
• List contents of directory you are in
ls
ls -a
ls -l
ls -lrt
lists names of directories/files
lists hidden files too
lists file details
lists recent files last
Save Some Time
Filename Completion
hit Tab key
should see
ls Des
ls Desktop
hit enter
History
hit
key
should see
ls Desktop
Changing Directories
mkdir practice
makes a new directory “practice”
ls -lrt
pwd
should see
cd practice
pwd
should see
ls
should see
/home/nmrclass
changes to directory “practice”
/home/nmrclass/practice
Nothing!
Changing Directories
Changing Directories
mkdir stuff
makes folder “stuff” inside practice
ls
should see “stuff”
Using an Editor
emacs mynotes.txt
If using a Mac:
open -e
Type: I could write a script.
File > Save (Buffer)
File > Exit emacs
ls
should see “mynotes.txt”
Format > Make plain text
File > Save
Using an Editor
gedit mynotes.txt
If using a Mac:
Type: I could write a script.
File > Save (Buffer)
File > Exit gedit
ls
should see “mynotes.txt”
Other Editors: pico
open -e
Format > Make plain text
File > Save
Using an Editor
Ctrl+C
&
Returns prompt
Runs program in background
gedit error.log &
Copying files
cp
cp --help
is the copy command
learn all the options or “arguments”
cp mynotes.txt stuff
cd stuff
ls
more mynotes.txt
Copying files
cp
cp --help
is the copy command
learn all the options or “arguments”
cp mynotes.txt stuff
cd stuff
ls
less mynotes.txt
Changing Directories
ls ..
ls ../..
shows one directory up
can also do (but don’t right now)
cd ..
goes up two!
pwd should see
cd ../..
/home/nmrclass/practice/stuff
Copying / Moving files
Could also use do:
cp mynotes.txt myothernotes.txt
mv myothernotes.txt hernotes.txt
mv hernotes.txt
..
Removing Files
pwd
should be in “stuff”
ls
rm mynotes.txt
ls
Using FreeSurfer
With FreeSurfer, certain variables must be
set in order to use it correctly:
FREESURFER_HOME
tell Operating System where FreeSurfer is
SUBJECTS_DIR
tell FreeSurfer where data is
What is a Variable?
• Character string that is assigned a value
• Way of passing information from the shell
to programs
• Assign a value to a variable
• Programs look “in the environment” for
variables
• Easy to change values/manipulate
What is a Variable?
How ‘echo’ works:
echo Freesurfer Rocks!
To set a variable:
setenv
TEST_VARIABLE yourfirstname
To check what a variable is set to:
echo
$TEST_VARIABLE
Using FreeSurfer
With FreeSurfer, certain variables must be
set in order to use it correctly:
FREESURFER_HOME
tell Operating System where FreeSurfer is
SUBJECTS_DIR
tell FreeSurfer where data is
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
Required Variables
• To use FreeSurfer you’ll have to do:
setenv
FREESURFER_HOME
/home/apps/freesurfer
tell Operating System where FreeSurfer is
source
source
$FREESURFER_HOME/SetUpFreeSurfer.csh
aka
/home/apps/freesurfer/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
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
Required Variables
• To use FreeSurfer you’ll have to do:
export FREESURFER_HOME=/home/apps/freesurfer
tell Operating System where FreeSurfer is
source
source
$FREESURFER_HOME/SetUpFreeSurfer.sh
aka
/home/apps/freesurfer/SetUpFreeSurfer.sh
source this script to get your computer
ready to use FreeSurfer (sources other
scripts & sets other variables)
export
SUBJECTS_DIR=/path/to/data
Required Variables
With FreeSurfer, certain variables must be
set in order to use it correctly:
FREESURFER_HOME
tell Operating System where FreeSurfer is
SUBJECTS_DIR
tell FreeSurfer where data is
echo
To check variables
$FREESURFER_HOME
echo
$SUBJECTS_DIR
Required Variables
setenv
SUBJECTS_DIR /path/to/data
To go to location of your data:
cd $SUBJECTS_DIR
$ means take the value of the variable
Required Variables
setenv
SUBJECTS_DIR /path/to/data
To go to location of your data:
cd $SUBJECTS_DIR
aka
cd /path/to/data
$ means take the value of the variable
Review
• 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
Review
• no double clicking
• mkdir
• ls
• cd
• pwd
• emacs, gedit, pico
• cp
• rm
More Help
• UNIX Tutorial For Beginners:
http://www.ee.surrey.ac.uk/Teaching/Unix/
• Linux in a Nutshell:
http://docstore.mik.ua/orelly/linux/lnut/ch01_01.htm
• UNIX Cheat Sheet:
http://tux.cs.unlv.edu/refs/linux_commands.html
• Command Line Tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/CommandL
ineNavigation
The End
Good Luck!
Intro to FreeSurfer Jargon
voxel
surface
volume
vertex
recon
cortical, subcortical
parcellation/segmentation
registration, morph, deform, transforms
(computing vs. resampling)
Intro to FreeSurfer Jargon
voxel
Intro to FreeSurfer Jargon
surface
Intro to FreeSurfer Jargon
surface
Intro to FreeSurfer Jargon
vertex
Recon
…short for reconstruction
…cortical surface reconstruction
…shows up in command recon-all
…“recon your data”
Recon
Volumes
orig.mgz
T1.mgz
brainmask.mgz wm.mgz
filled.mgz
(Subcortical Mass)
Cortical vs. Subcortical GM
cortical gm
subcortical gm
sagittal
coronal
Cortical vs. Subcortical GM
subcortical gm
sagittal
coronal
Parcellation vs. Segmentation
(cortical) parcellation
(subcortical) segmentation
Intro to FreeSurfer Jargon
voxel
surface
volume
vertex
recon
cortical, subcortical
parcellation/segmentation
registration, morph, deform, transforms
(computing vs. resampling)
FreeSurfer Questions
Search for terms and answers
to all your questions in the Glossary, FAQ,
or
FreeSurfer Mailing List Archives
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
Inter-subject, uni-modal
example
target
Flirt 612/13/2011
DOF
subject
Flirt 9 DOF
Flirt 12 DOF
Linear registration: 6, 9, 12
DOF
target
subject
Flirt 12
DOF
9
6 DOF
Linear registration: 6, 9, 12
DOF
Flirt
6dof
9dof
subject
target
Flirt 12 DOF
Linear registration: 6, 9, 12
DOF
Flirt
6 DOF
9
target
subject
Flirt 12 DOF
Intra-subject, multi-modal
example
before spatial alignment
after spatial alignment
before spatial alignment
after spatial alignment
before spatial alignment
after spatial alignment
Inter-subject non-linear
example
target
CVS reg
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
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 FreeSurfer
echo I love $name !
% chmod u+x my_first_script.csh
% ./my_first_script.csh
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
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 parameters
echo parameter 1 is $1
echo parameter 2 is $2
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
Registration
-align subjects
-common space
-reference points b/w subjects will be same
transforms
template
deform
morph
warp
compute
resample
More Help
alias e emacs
man alias
ls file*  lists file1, file2, file3
ls file[12]  lists file1 and file2 but not file3
command >>& file.txt  save output to screen and errors
in text file