Center for Cognitive Neuroscience - User contributions [en]

Using Screen

2014-04-23T20:39:59Z

Ccn admin: /* Quick Start */

==What is Screen?==
From the [http://www.gnu.org/software/screen/ Gnu Screen] home page.

<blockquote>Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells. Each virtual terminal provides the functions of the DEC VT100 terminal and, in addition, several control functions from the ANSI X3.64 (ISO 6429) and ISO 2022 standards (e.g., insert/delete line and support for multiple character sets). There is a scrollback history buffer for each virtual terminal and a copy-and-paste mechanism that allows the user to move text regions between windows. When screen is called, it creates a single window with a shell in it (or the specified command) and then gets out of your way so that you can use the program as you normally would. Then, at any time, you can create new (full-screen) windows with other programs in them (including more shells), kill the current window, view a list of the active windows, turn output logging on and off, copy text between windows, view the scrollback history, switch between windows, etc. All windows run their programs completely independent of each other. Programs continue to run when their window is currently not visible and even when the whole screen session is detached from the users terminal.</blockquote>

==Quick Start==
Login to Hoffman2 (Make sure you keep track of your Login Node Number)
$ ssh user@hoffman2.idre.ucla.edu
$ screen #- Start Screen Session

Launch a QRSH (if on hoffman2) session:
$ qrsh -l h_data=4G

Run bash/matlab script.

(While Computing :)
CTRL+A d #- detach the screen session

$ screen -list #- list all screen sessions. EXAMPLE OUTPUT 9368.ttyp1.cohen-static (Detached)

$ screen -r 9368 #- Resume a screen session with an id of 9368 (see EXAMPLE above)

== Setup ==
First copy/paste the following configuration into a file and then save it as .screenrc in your Home directory (for osx users that's /Users/username/).

<code><pre>
# .screenrc
# Dave Kaufman
# http://davekaufman.net
#
# Created: 1 Jul 2002 04:00:00 PM EDT
# Last Modified: Sat 22 Jan 2005 11:41:18 PM EST
#
# This file is used to initialize screen sessions

# No annoying audible bell, using "visual bell"
#vbell on # default: off
#vbell_msg " -- Ring, Ring!! -- " # default: "Wuff,Wuff!!"

# Automatically detach on hangup.
autodetach on # default: on

# Don't display the copyright page
startup_message off # default: on

# Affects the copying of text regions
crlf off # default: off

# Change default scrollback value for new windows
defscrollback 1000 # default: 100

# Define the time that all windows monitored for silence should
# wait before displaying a message. Default 30 seconds.
silencewait 15

# Ensures that the default shell is the same as the value of the $SHELL env variable
shell -$SHELL

# emulate .logout message
pow_detach_msg "Screen session of \$LOGNAME \$:cr:\$:nl:ended."

# Pretty status bar at the bottom.
hardstatus alwayslastline
hardstatus string "%{gk}[ %{G}%H %{g}][%= %{wk}%?%-Lw%?%{r}(%{W}%n*%f %t%?(%u)%?%{r})%{w}%?%+Lw%?%?%= %{g}][%{B} %m/%d %{W}%c %{g}]"
# XTERM TWEAKS
# ===============================================================

# xterm understands both im/ic and doesn't have a status line.
# Note: Do not specify im and ic in the real termcap/info file as
# some programs (e.g. vi) will not work anymore.
termcap xterm hs@:cs=\E[%i%d;%dr:im=\E[4h:ei=\E[4l
terminfo xterm hs@:cs=\E[%i%p1%d;%p2%dr:im=\E[4h:ei=\E[4l

# 80/132 column switching must be enabled for ^AW to work
# change init sequence to not switch width
termcapinfo xterm Z0=\E[?3h:Z1=\E[?3l:is=\E[r\E[m\E[2J\E[H\E[?7h\E[?1;4;6l

# Make the output buffer large for (fast) xterms.
# termcapinfo xterm* OL=10000
termcapinfo xterm* OL=100

# tell screen that xterm can switch to dark background and has function
# keys.
termcapinfo xterm 'VR=\E[?5h:VN=\E[?5l'
termcapinfo xterm 'k1=\E[11~:k2=\E[12~:k3=\E[13~:k4=\E[14~'
termcapinfo xterm 'kh=\EOH:kI=\E[2~:kD=\E[3~:kH=\EOF:kP=\E[5~:kN=\E[6~'

# special xterm hardstatus: use the window title.
termcapinfo xterm 'hs:ts=\E]2;:fs=\007:ds=\E]2;screen\007'

#terminfo xterm 'vb=\E[?5h$<200/>\E[?5l'
termcapinfo xterm 'vi=\E[?25l:ve=\E[34h\E[?25h:vs=\E[34l'

# emulate part of the 'K' charset
termcapinfo xterm 'XC=K%,%\E(B,[\304,\\\\\326,]\334,{\344,|\366,}\374,~\337'

# xterm-52 tweaks:
# - uses background color for delete operations
termcapinfo xterm* be

# WYSE TERMINALS
# ===============================================================

#wyse-75-42 must have flow control (xo = "terminal uses xon/xoff")
#essential to have it here, as this is a slow terminal.
termcapinfo wy75-42 xo:hs@

# New termcap sequences for cursor application mode.
termcapinfo wy* CS=\E[?1h:CE=\E[?1l:vi=\E[?25l:ve=\E[?25h:VR=\E[?5h:VN=\E[?5l:cb=\E[1K:CD=\E[1J

# OTHER TERMINALS
# ===============================================================

# make hp700 termcap/info better
termcapinfo hp700 'Z0=\E[?3h:Z1=\E[?3l:hs:ts=\E[62"p\E[0$~\E[2$~\E[1$}:fs=\E[0}\E[61"p:ds=\E[62"p\E[1$~\E[61"p:ic@'

# Extend the vt100 desciption by some sequences.
termcap vt100* ms:AL=\E[%dL:DL=\E[%dM:UP=\E[%dA:DO=\E[%dB:LE=\E[%dD:RI=\E[%dC
terminfo vt100* ms:AL=\E[%p1%dL:DL=\E[%p1%dM:UP=\E[%p1%dA:DO=\E[%p1%dB:LE=\E[%p1%dD:RI=\E[%p1%dC
termcapinfo linux C8
# old rxvt versions also need this
# termcapinfo rxvt C8

# Change the escape key for hotkeys so I can run screen within screen
# escape ^l\\
# Let's remove some dangerous key bindings ...
bind k
bind ^k
bind .
bind ^\
bind \\
bind ^h
bind h

# ... and make them better.
bind 'K' kill
bind 'I' login on
bind 'O' login off
bind '}' history
bind 'Q' quit

# Yet another hack:
# Prepend/append register [/] to the paste if ^a^] is pressed.
# This lets me have autoindent mode in vi.
register [ "\033:se noai\015a"
register ] "\033:se ai\015a"
bind ^] paste [.]

# Resize the current region. The space will be removed from or added to
# the region below or if there's not enough space from the region above.
bind = resize =
bind + resize +3
bind - resize -3

# Time a message is displayed if screen is not disturbed by
# other activity. The dafault is 5 seconds:
msgwait 15

# change the default activity message to include a bell.
activity "Activity in %n ^G"

# Don't you want to start programs which need a DISPLAY ?
setenv DISPLAY ':0'

# Bind F11 and F12 (NOT F1 and F2) to previous and next screen window
bindkey -k F1 prev
bindkey -k F2 prev

# Default Buffers
screen -M -t Shell 0
screen -t Shell 1
screen -t Shell 2
screen -t Shell 3
select 0
</pre></code>

Then all that is left is to run it. Screen is included by default in every OSX package and is available in any package manager I've seen (ports, portage, rpm, etc). If your using OSX, just type the following at the command prompt:

$ screen

==No, not how do I start it. How do I use it?==
Ah, yeah, I suppose that would help. Here's a quick run down of the basics. After starting screen hit your space bar to exit out of the welcome screen. You'll see what looks like a normal run of the mill terminal session. If you copy/pasted the configuration file above you'll also see a very convenient bar at the bottom that tells you which screen window your currently in, how many you have, and the name of your computer.

All that is left is moving between these sessions, creating new ones, deleting old ones, and the holy grail of detaching and resuming sessions.

CTRL+A 1 - move to screen 1

CTRL+A 2 - move to screen 2

CTRL+A <num> - move to the screen with number <num>, e.g. 3, 4, 5, 6, <num>

CTRL+A X - move to screen X where X is a screen number

CTRL+A n - move to the (n)ext screen

CTRL+A c - (c)reate a new screen

$ exit - exit the current screen window (not the entire screen program, just that window)

CTRL+A d - detach the screen session

$ screen -list - list all screen sessions. EXAMPLE OUTPUT 9368.ttyp1.cohen-static (Detached)

$ screen -r 9368 - Resume a screen session with an id of 9368 (see EXAMPLE above)

==External Links==
*[http://www.kb.indiana.edu/data/acuy.html Indiana University UITS (additional information about screen)]
*[http://www.gnu.org/software/screen GNU Screen Homepage]

Hoffman2:Profile

2014-04-23T01:24:51Z

Ccn admin: /* Changing Passwords */

[[Hoffman2|Back to all things Hoffman2]]

In UNIX systems, there are certain configuration files that get executed every time you login. If you are using the Bash shell (default), you have a file called <code>.bash_profile</code> which is processed when you log in. In order to make the FMRI toolset available to you on Hoffman2 and so you can work well with others, we recommend that you follow the instructions in the [[Hoffman2:Profile#Basics|Basics section]]. Read [[Hoffman2:Profile#Extras|Extras]] for some bells and whistles.

==Basics==
You account has one last thing that needs to be edited before being usable.

# [[Hoffman2:Accessing the Cluster#SSH - Command Line|SSH into Hoffman2]]
# Use your favorite [[Text Editors|text editor]] to edit the file <code>~/.bash_profile</code>
#: [[Text Editors#Vim (H2) (OSX)|VIM]]
#:* <pre>$ vim ~/.bash_profile</pre>
#: [[Text Editors#Emacs (H2) (OSX)|Emacs]]
#:* <pre>$ emacs ~/.bash_profile</pre>
#: [[Text Editors#NEdit (H2) (OSX)|NEdit]]
#:* <pre>$ nedit ~/.bash_profile</pre>
# Insert these lines at the '''bottom''' of the file
#:* <pre>source /u/home/FMRI/apps/etc/profile
umask 007</pre>
#: [[Text Editors#Vim (H2) (OSX)|VIM]]
#:* Type <code>G</code> - capital G - to go to the end of the file
#:* Type <code>A</code> - capital A - to go to the end of the line and enter insert mode
#:* Type <code>ENTER</code> - to insert a newline
#:* Type or paste in the specified lines.
#: [[Text Editors#Emacs (H2)(OSX)|Emacs]]
#:* Use the arrow keys to scroll the cursor down to the bottom of the document and add a newline.
#:* Type or paste in the specified lines.
#: [[Text Editors#NEdit (H2)|NEdit]]
#:* Use the arrow keys to scroll the cursor down to the bottom of the document and add a newline.
#:* Type or paste in the specified lines.
# Save the file
#: [[Text Editors#Vim (H2) (OSX)|VIM]]
#:* <code>ESC + ":wq" + ENTER</code>
#: [[Text Editors#Emacs (H2) (OSX)|Emacs command line]]
#:* <code>CTRL+x, CTRL+c</code>
#: [[Text Editors#Emacs (H2) (OSX)|Emacs GUI]]
#:* <code>CTRL+x, CTRL+c, y</code>
#:* or use the menu system
#: [[Text Editors#NEdit (H2)|NEdit]]
#:* Use the menu.
# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.

===Curious?===
For those that care, what you are doing is asking the computer to execute the file
/u/home/FMRI/apps/etc/profile
every time you login. This file modifies your PATH variable so you have access to the FMRI toolset.

The last line
umask 007
makes it so that any files you create will not allow "anyone" outside your group to read, write, or execute files and directories you make. This does not automatically grant read, write, and execute privileges to you and your group though.

==Extras==
===Collaboration===
By default, any files and directories you create will not necessarily have permissions that allow your group to write on them. This can be a problem if other people are supposed to build on data you processed. We have a script ([[Hoffman2:Scripts:fix_perms.sh |fix_perms.sh]]) that will kindly find any files you own in a specified directory that don't have read/write/execute permissions for the group and make it so they do.

You can build this script into your bash profile so that every time you log into Hoffman2, it will run in the background. It is also recommended that you run this script at the end of jobs to make results immediately available to collaborators.

Adding the line
fix_perms.sh -q /u/home/[GROUP]/data &
to the end of your bash profile will run the permission fixer on your group's common data directory in the background quietly each time you log in. '''Make sure to replace [GROUP] with the name of your Hoffman2 group (e.g. mscohen, sbook, cbearden, laltshul, jfeusner or mgreen).'''

===Colors===
You can change the content and color of your command prompt by editing your bash_profile. There is a great explanation of how to do this [http://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html here].

Some of the content you can include in the command prompt:
;Current time
: You can format this however you want. This helps when looking back through your Terminal to find when you made certain changes to files.
;Current working directory
: So you always know where you are in a filesystem and don't need to constantly retype <code>pwd</code>.
;Username
: Who you are. Helpful if you are logged into multiple servers under multiple accounts and need help keeping track.
;Host
: The name of the computer you are logged into. This also helps you know where you are at all times.

Line to add to your bash profile
export PS1="\[\e[0;31m\]\h\[\e[1;37m\]:\[\e[1;34m\]\w\n\[\e[1;37m\]\D{%Y-%m-%d-%H-%M-%S} \[\e[22;32m\]\u \$ "
Resulting prompt (on a black background) 
<code style="background:#000000; padding:5pt">HOST:CURRENT WORKING DIRECTORY 
 DATETIME IN ISO8601 FORMAT USERNAME $</code>

==Example Bash Profile==
<nowiki>#.bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

# Source to use FMRI Apps
source /u/home/FMRI/apps/etc/profile

# Umask (Revoke Permissions)
umask 007

# Collaborative permissions (Replace collabDirectory with your project Directory)
fix_perms.sh -q /u/home/sbook/data/collabDirectory &

# Happy Colors
export PS1="\[\e[0;31m\]\h\[\e[1;37m\]:\[\e[1;34m\]\w\n\[\e[1;37m\]\D{%Y-%m-%d-%H-%M-%S} \[\e[22;32m\]\u \$ "

# Fix for QRSH when consolidating job output files
alias qrsh='qrsh -o /dev/null'
</nowiki>

== Changing Passwords ==
Use the command below to change password. It will prompt you for your old password, and then the new password.
$ passwd
Changing password for user joebruin.
Please enter your current password:
Please enter your new password:

==External Links==
*[http://ss64.com/bash/period.html Explanation of source]
*[http://linux.die.net/man/2/umask Man for umask]
*[http://www.cyberciti.biz/tips/understanding-linux-unix-umask-value-usage.html Better explanation of umask]
*[http://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html Coloration]
*[http://en.wikipedia.org/wiki/ISO_8601 ISO 8601 Datetime format]

Hoffman2:Profile

2014-04-23T01:24:20Z

Ccn admin: /* Changing Passwords */

Hoffman2:Getting an Account

2014-04-23T01:23:44Z

Ccn admin:

[[Hoffman2|Back to all things Hoffman2]]

==UCLA Grid Portal==
The UCLA Grid Portal provides access to many clusters hosted at UCLA. By registering for an account, not only do you gain access to the Hoffman2 cluster and any other member clusters by request, but you also gain access to a variety of shared resources including matlab, R, Octave, Mathematica, FSL, and many more at UCLA and the UC system in general. Yes, the Grid Portal is a multi-university effort spanning from Northern to Southern California.

You will probably be amazed at the resources you gain simply by signing up for the Grid Portal. For further information, please visit the [https://grid.ucla.edu:9443/gridsphere/gridsphere?cid=home&JavaScript=enabled Grid Portal] home page.

==Requesting Hoffman2 Account==
===What you need===
A UCLA BOL account, available for free to any UCLA staff, student, or faculty member. If you do not have a BOL account, head to the [http://www.bol.ucla.edu/ UCLA BOL] services page. '''Click on "Create UCLA Logon ID" under "UCLA Logon ID Utilities"'''

===Applying for the Account===
ATTENTION: If you are a member of another lab or are a PI interested in obtaining Hoffman access, please see the section
[[#Becoming A Faculty Sponsor | Becoming a Faculty Sponsor]]
#Navigate to the [http://hpc.ucla.edu/hoffman2/getting-started/getting-started.php Account Applications] page.
#Read over the application summary
#Click "New User Registration"
#Authenticate using your UCLA BOL username and pass
#Fill out the form with appropriate information. Please read the information at the top of the form to familiarize yourself with the process of gaining an account. For Hoffman2, your Faculty Sponsor should be Mark Cohen, Alison Burggren (for Susan Bookheimer's lab), or your respective PI if they have created an account on Hoffman.
;Proposed UserName
:This will be the name you use to sign into the cluster
;Select a Resource
:For the Mark Cohen/Susan Bookheimer labs, choose "Hoffman2". However, you can request access to any cluster that is a member of the Grid Portal.

Click Submit and you are done.
You will receive an email with a link to a temporary password. PLEASE WRITE IT DOWN. The link expires after 72 hours. You can change your password by going to [[ Hoffman2:Profile#Changing_Passwords | Here. ]]

==Becoming A Faculty Sponsor==
If you are a PI or Lab Manager interested in the Hoffman2 server, you will want to create a Faculty Sponsor account first. Also, if you are a member of another lab collaborating with the Cohen or Bookheimer labs, you may want to forward this information to your PI or Lab Manager. Faculty Sponsors can approve (or deny) applications for membership to their group. They also receive a group folder and a unique group id so their users can work and share data easily with each other.

#Navigate to the [http://www.ats.ucla.edu/clusters/common/account_applications/cluster.htm Account Applications] page.
#Read over the application summary
#Click "Request to become faculty sponsor"
#Fill out the form with appropriate information.

Under 'Reason', about any generic reason is appropriate for faculty members. For example, "To perform fMRI analysis." will likely suffice.

== Change Passwords ===

==External Links==
*[https://grid.ucla.edu:9443/gridsphere/gridsphere?cid=home&JavaScript=enabled UCLA Grid Portal]
*[http://www.bol.ucla.edu/ UCLA BOL Home Page]
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Home Page]

Hoffman2:Getting an Account

2014-04-23T01:22:17Z

Ccn admin:

[[Hoffman2|Back to all things Hoffman2]]

==UCLA Grid Portal==
The UCLA Grid Portal provides access to many clusters hosted at UCLA. By registering for an account, not only do you gain access to the Hoffman2 cluster and any other member clusters by request, but you also gain access to a variety of shared resources including matlab, R, Octave, Mathematica, FSL, and many more at UCLA and the UC system in general. Yes, the Grid Portal is a multi-university effort spanning from Northern to Southern California.

You will probably be amazed at the resources you gain simply by signing up for the Grid Portal. For further information, please visit the [https://grid.ucla.edu:9443/gridsphere/gridsphere?cid=home&JavaScript=enabled Grid Portal] home page.

==Requesting Hoffman2 Account==
===What you need===
A UCLA BOL account, available for free to any UCLA staff, student, or faculty member. If you do not have a BOL account, head to the [http://www.bol.ucla.edu/ UCLA BOL] services page. '''Click on "Create UCLA Logon ID" under "UCLA Logon ID Utilities"'''

===Applying for the Account===
ATTENTION: If you are a member of another lab or are a PI interested in obtaining Hoffman access, please see the section
[[#Becoming A Faculty Sponsor | Becoming a Faculty Sponsor]]
#Navigate to the [http://hpc.ucla.edu/hoffman2/getting-started/getting-started.php Account Applications] page.
#Read over the application summary
#Click "New User Registration"
#Authenticate using your UCLA BOL username and pass
#Fill out the form with appropriate information. Please read the information at the top of the form to familiarize yourself with the process of gaining an account. For Hoffman2, your Faculty Sponsor should be Mark Cohen, Alison Burggren (for Susan Bookheimer's lab), or your respective PI if they have created an account on Hoffman.
;Proposed UserName
:This will be the name you use to sign into the cluster
;Select a Resource
:For the Mark Cohen/Susan Bookheimer labs, choose "Hoffman2". However, you can request access to any cluster that is a member of the Grid Portal.

Click Submit and you are done.
You will receive an email with a link to a temporary password. PLEASE WRITE IT DOWN. The link expires after 72 hours. [[ Hoffman2:Profile#Changing_Passwords | How to change Passwords. ]]
==Becoming A Faculty Sponsor==
If you are a PI or Lab Manager interested in the Hoffman2 server, you will want to create a Faculty Sponsor account first. Also, if you are a member of another lab collaborating with the Cohen or Bookheimer labs, you may want to forward this information to your PI or Lab Manager. Faculty Sponsors can approve (or deny) applications for membership to their group. They also receive a group folder and a unique group id so their users can work and share data easily with each other.

#Navigate to the [http://www.ats.ucla.edu/clusters/common/account_applications/cluster.htm Account Applications] page.
#Read over the application summary
#Click "Request to become faculty sponsor"
#Fill out the form with appropriate information.

Under 'Reason', about any generic reason is appropriate for faculty members. For example, "To perform fMRI analysis." will likely suffice.

== Change Passwords ===

==External Links==
*[https://grid.ucla.edu:9443/gridsphere/gridsphere?cid=home&JavaScript=enabled UCLA Grid Portal]
*[http://www.bol.ucla.edu/ UCLA BOL Home Page]
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Home Page]

Hoffman2:Profile

2014-04-23T01:18:00Z

Ccn admin:

[[Hoffman2|Back to all things Hoffman2]]

In UNIX systems, there are certain configuration files that get executed every time you login. If you are using the Bash shell (default), you have a file called <code>.bash_profile</code> which is processed when you log in. In order to make the FMRI toolset available to you on Hoffman2 and so you can work well with others, we recommend that you follow the instructions in the [[Hoffman2:Profile#Basics|Basics section]]. Read [[Hoffman2:Profile#Extras|Extras]] for some bells and whistles.

==Basics==
You account has one last thing that needs to be edited before being usable.

# [[Hoffman2:Accessing the Cluster#SSH - Command Line|SSH into Hoffman2]]
# Use your favorite [[Text Editors|text editor]] to edit the file <code>~/.bash_profile</code>
#: [[Text Editors#Vim (H2) (OSX)|VIM]]
#:* <pre>$ vim ~/.bash_profile</pre>
#: [[Text Editors#Emacs (H2) (OSX)|Emacs]]
#:* <pre>$ emacs ~/.bash_profile</pre>
#: [[Text Editors#NEdit (H2) (OSX)|NEdit]]
#:* <pre>$ nedit ~/.bash_profile</pre>
# Insert these lines at the '''bottom''' of the file
#:* <pre>source /u/home/FMRI/apps/etc/profile
umask 007</pre>
#: [[Text Editors#Vim (H2) (OSX)|VIM]]
#:* Type <code>G</code> - capital G - to go to the end of the file
#:* Type <code>A</code> - capital A - to go to the end of the line and enter insert mode
#:* Type <code>ENTER</code> - to insert a newline
#:* Type or paste in the specified lines.
#: [[Text Editors#Emacs (H2)(OSX)|Emacs]]
#:* Use the arrow keys to scroll the cursor down to the bottom of the document and add a newline.
#:* Type or paste in the specified lines.
#: [[Text Editors#NEdit (H2)|NEdit]]
#:* Use the arrow keys to scroll the cursor down to the bottom of the document and add a newline.
#:* Type or paste in the specified lines.
# Save the file
#: [[Text Editors#Vim (H2) (OSX)|VIM]]
#:* <code>ESC + ":wq" + ENTER</code>
#: [[Text Editors#Emacs (H2) (OSX)|Emacs command line]]
#:* <code>CTRL+x, CTRL+c</code>
#: [[Text Editors#Emacs (H2) (OSX)|Emacs GUI]]
#:* <code>CTRL+x, CTRL+c, y</code>
#:* or use the menu system
#: [[Text Editors#NEdit (H2)|NEdit]]
#:* Use the menu.
# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.

===Curious?===
For those that care, what you are doing is asking the computer to execute the file
/u/home/FMRI/apps/etc/profile
every time you login. This file modifies your PATH variable so you have access to the FMRI toolset.

The last line
umask 007
makes it so that any files you create will not allow "anyone" outside your group to read, write, or execute files and directories you make. This does not automatically grant read, write, and execute privileges to you and your group though.

==Extras==
===Collaboration===
By default, any files and directories you create will not necessarily have permissions that allow your group to write on them. This can be a problem if other people are supposed to build on data you processed. We have a script ([[Hoffman2:Scripts:fix_perms.sh |fix_perms.sh]]) that will kindly find any files you own in a specified directory that don't have read/write/execute permissions for the group and make it so they do.

You can build this script into your bash profile so that every time you log into Hoffman2, it will run in the background. It is also recommended that you run this script at the end of jobs to make results immediately available to collaborators.

Adding the line
fix_perms.sh -q /u/home/[GROUP]/data &
to the end of your bash profile will run the permission fixer on your group's common data directory in the background quietly each time you log in. '''Make sure to replace [GROUP] with the name of your Hoffman2 group (e.g. mscohen, sbook, cbearden, laltshul, jfeusner or mgreen).'''

===Colors===
You can change the content and color of your command prompt by editing your bash_profile. There is a great explanation of how to do this [http://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html here].

Some of the content you can include in the command prompt:
;Current time
: You can format this however you want. This helps when looking back through your Terminal to find when you made certain changes to files.
;Current working directory
: So you always know where you are in a filesystem and don't need to constantly retype <code>pwd</code>.
;Username
: Who you are. Helpful if you are logged into multiple servers under multiple accounts and need help keeping track.
;Host
: The name of the computer you are logged into. This also helps you know where you are at all times.

Line to add to your bash profile
export PS1="\[\e[0;31m\]\h\[\e[1;37m\]:\[\e[1;34m\]\w\n\[\e[1;37m\]\D{%Y-%m-%d-%H-%M-%S} \[\e[22;32m\]\u \$ "
Resulting prompt (on a black background) 
<code style="background:#000000; padding:5pt">HOST:CURRENT WORKING DIRECTORY 
 DATETIME IN ISO8601 FORMAT USERNAME $</code>

==Example Bash Profile==
<nowiki>#.bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

# Source to use FMRI Apps
source /u/home/FMRI/apps/etc/profile

# Umask (Revoke Permissions)
umask 007

# Collaborative permissions (Replace collabDirectory with your project Directory)
fix_perms.sh -q /u/home/sbook/data/collabDirectory &

# Happy Colors
export PS1="\[\e[0;31m\]\h\[\e[1;37m\]:\[\e[1;34m\]\w\n\[\e[1;37m\]\D{%Y-%m-%d-%H-%M-%S} \[\e[22;32m\]\u \$ "

# Fix for QRSH when consolidating job output files
alias qrsh='qrsh -o /dev/null'
</nowiki>

== Changing Passwords ==
Use the command below to change password. It will prompt you for your old password, and then the new password.
$ passwd

==External Links==
*[http://ss64.com/bash/period.html Explanation of source]
*[http://linux.die.net/man/2/umask Man for umask]
*[http://www.cyberciti.biz/tips/understanding-linux-unix-umask-value-usage.html Better explanation of umask]
*[http://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html Coloration]
*[http://en.wikipedia.org/wiki/ISO_8601 ISO 8601 Datetime format]

Hoffman2:Introduction

2014-04-23T01:11:48Z

Ccn admin: /* Computing Nodes */

[[Hoffman2|Back to all things Hoffman2]]

==What is Hoffman2?==
The Hoffman2 Cluster is a campus computing resource at UCLA and is named for Paul Hoffman (1947-2003). It is maintained by the Academic Technology Services Department at UCLA and they host a webpage about it [http://www.ats.ucla.edu/clusters/hoffman2/ here]. With many high end processors and data storage and backup technologies, it is a useful tool for executing research computations especially when working with large datasets. More than 1000 users are currently registered and the cluster sees tremendous usage. Click [[Hoffman2:Getting an Account|here]] to find out how to join that user group. In February 2012 alone, there were more than 4 million compute hours logged. See more usage statistics [https://idre.ucla.edu/hoffman2/cluster-statistics here].

==Anatomy of the Computing Cluster==
What does Hoffman2 consist of?
* Login Nodes
* Computing Nodes
* Storage Space
* Sun Grid Engine (a brain of sorts)

[[File:hoffman2layout.png]]
 
''**Image taken from a previous ATS "Using Hoffman2 Cluster" slide deck and modified for our point.**''

===Login Nodes===
There are four login nodes which allow you to access and interact with the Hoffman2 Cluster. These are essentially four dedicated computers that you can [[Hoffman2:Accessing the Cluster#SSH|SSH]] into and use to look at and edit your files or submit computing jobs to the queue (more on what the queue is in a bit). It is important to remember that these are four computers being shared by ALL the Hoffman2 users. Doing ANY type of heavy computing on these nodes is frowned upon. If you are:
*moving lots of files
*calculating the inverse solution to an EEG signal, or
*running a bunch of python scripts to extract tractography of a brain
you should NOT be doing this on a login node. If the sysadmins at ATS find any process that is taking up too many resources on the login nodes, they reserve the right to terminate the process immediately.

===Computing Nodes===
As of April 2014, Hoffman2 is made up of more than 12000 processors across three data centers and this number continues to grow as the cluster is expanded. [http://hpc.ucla.edu/hoffman2/h2stat/h2stat.php Stats.] The individual cores of the processors are where your programs gets executed when you submit a job to the cluster. There are ways to request that you only be given one core to use or that you be given many cores.

There is also a GPU cluster that has more than 300 nodes, but access to this must be requested separately from a normal Hoffman2 account. Look [http://fuji.ats.ucla.edu/for-transfer/hoffman2-cluster/computing/gpuq.htm here] for how to request access.

The reason the number of computing cores continues to grow is because more resource groups (like individual research labs) join Hoffman2 and buy nodes to be integrated into the cluster. Nodes contributed by a resource group are guaranteed to that resource group and can be used to run longer jobs ([http://fuji.ats.ucla.edu/for-transfer/hoffman2-cluster/computing/policies.htm#highp up to 14 days]). As of June 2013, the Cohen and Bookheimer groups on Hoffman2 have 96 cores:
* 6 nodes (installed pre 2010) each with
** 8 cores
** 8GB RAM
* 3 nodes (installed Fall 2012) each with
** 16 cores
** 48GB RAM
Use the command <code>mygroup</code> to see what resources you have available.

===Storage Space===
For official and up-to-date information about storage space, [https://idre.ucla.edu/hoffman2/data-storage click here]. If you want a quick overview, see below.

====Long Term Storage====
ATS maintains high end storage systems (BlueArc and Panasas) for Hoffman2 disk space. There have built in redundancies and are fault tolerant. On top of that, ATS does tape backups regularly.

If all of that sounded Greek to you, the important thing to understand is that there is a lot of disk space on Hoffman2 and ATS takes great pains to make sure your data is safe.

=====Home Directories=====
:When you login to Hoffman2, you get dropped into your home directory immediately. Home directory locations follow the pattern
::<code>/u/home/[u]/[username]</code>
:Where <code>[u]</code> is the first letter of the username, e.g.
::<code>/u/home/j/jbruin</code>
::<code> /u/home/t/ttrojan</code>

:Your home directory is where you can keep your personal files (papers, correspondences, notes, etc.) and files you frequently change (source code, configuration files, job command files). '''It is not the place for your large datasets for computing.''' Data in your home directory is accessible from all login and computing nodes.

:Every user is allowed to store up to 20GB of data files in their home directory. If you are part of a cluster contributing group, you can also store data files in that group's common space described in the next section...

:[[Hoffman2:Quotas|Find out how much space your group is using on Hoffman2.]]

=====Group Directory=====
:Group directories are given to groups that purchase extended storage space (in 1TB/1million file increments for three year periods, as of Summer 2013). This is common space designed for collaboration and is where your datasets should mainly be stored. Individual users are given directories under the main group directory to help organize data ownership. For example:
::<pre>/u/home/mscohen # Common group directory</pre>
::<pre>/u/home/mscohen/data # Common group "data" directory, create subdirectories within this for specific projects or uses</pre>
::<pre>/u/home/mscohen/aaronab # mscohen group directory for the user aaronab, different from their /u/home/a/aaronab home directory</pre>
::<pre>/u/home/mscohen/kerr # mscohen group directory for the user kerr, different from their /u/home/k/kerr home directory</pre>
::<pre>/u/home/mscohen/pamelita # mscohen group directory for the user pamelita, different from their /u/home/p/pamelita home directory</pre>
:and these directories are accessible from all login and computing nodes.

:'''These directories have limits to how many files can be put in them and how large those files can be.'''
:*When a group buys in for 1TB/1million files, their quota is considered met when they have EITHER
:** 1TB worth of files, OR
:** 1 million files
:*When a group buys in for 4TB/4million files, their quota is considered met when they have EITHER
:** 4TB worth of files, OR
:** 4 million files
:'''Once a group's quota has been reached, everyone in that group is immediately prevented from creating any more files in the group directory automatically.''' This means any computing jobs you are running may fail due to an inability to write out their results. You may also have trouble starting GUI sessions due to an inability to create temporary files.
:Read about how to monitor your disk quota [[Hoffman2:Quotas|here]].

=====Historical Notes=====
======June 2013======
: ''Before July 2013, for users that were part of groups that purchased storage, their home directories were the same as their personal group directories. e.g.''
::<code> /u/home/j/jbruin</code>
:''did not exist, but''
::<code> /u/home/mscohen/jbruin</code>
:''did exist and was the home directory (and personal group directory) for the user jbruin. IDRE changed this behavior after the Summer Maintenance restart in 2013 to better separate users from their groups. This separation more cleanly allows users to be part of multiple storage groups (e.g. belonging to sbook and mscohen groups), or switch between single groups over time, while retaining their own personal space on the cluster. A symlink named '''project''' was placed in the new home directories pointing to the old home directories. e.g.''
::<code> /u/home/j/jbruin/project -> /u/home/mscohen/jbruin</code>

======June 2011======
: ''Before July 2011, there was a symlink pointing from /u/home9 to /u/home as a legacy support mechanism. This symlink was finally removed after the Summer Maintenance of 2011 and some adjustments had to be made by anyone still using home9 references.''

====Temporary Storage====
When running a computing job on Hoffman2, reading and writing a bunch of files in your home directory can be slow. So faster temporary storage is available to use for ongoing jobs. Read the official description [https://idre.ucla.edu/hoffman2/data-storage#tempfs here].

=====work=====
:'''/work'''
:Each computing node has its own unique "work" directory. This is only accessible by jobs on that specific node. Any data your job may put on it will be removed as soon as your job finishes. There is at least 100GB of this space on each node, but you may only use a portion proportional to the number of cores you are using on that node (you have to share).

:Every job is given a unique subdirectory on ''work'' where it can read and write files rapidly. The [[Hoffman2:UNIX Tutorial#Environment Variables|UNIX environment variable]] <code>$TMPDIR</code> points to this directory.

:If your job reads from or writes to a file repeatedly, you may save time by keeping that file in this temporary directory and then moving it to your home directory at completion so it is not deleted.

=====scratch=====
:'''/u/scratch/[u]/[username]'''
:Where ''[username]'' is replaced with your Hoffman2 username and ''[u]'' is replaced with the first letter of your username. Data here is accessible on all login and computing nodes. You can use up to 2TB of space here, but data is not kept here for more than 7 days and can be overwritten sooner if there is a high demand for scratch space. Use the [[Hoffman2:UNIX Tutorial#Environment Variables|UNIX environment variable]] <code>$SCRATCH</code> to reliably access your personal scratch directory.

===Sun Grid Engine===
The Sun Grid Engine is the brains behind how jobs get executed on the cluster. When you request that a script be run on Hoffman2, the SGE looks at the resources you requested (how much memory, how many computing cores, how many computing hours, etc) and puts your job in a queue (a waiting line for those not familiar with British English) based on your requirements. Less demanding jobs generally get front loaded while more demanding ones must wait for adequate resources to free up. The SGE tries to schedule jobs on computing nodes in order to make the most efficient use of the resources available.

====Queues====
There is more than one queue on Hoffman2. Each is for a slightly different purpose:
; express
: For jobs requesting at most 2 hours of computing time.
; interactive
: For jobs requesting at most 24 hours of computing time and requiring the ability for users to interact with the program running.
; highp
: For jobs requesting at most 14 days of computing time. These are required to run on nodes owned by your group.
And there are others. Read about them [http://fuji.ats.ucla.edu/for-transfer/hoffman2-cluster/computing/policies.htm here].

[[Hoffman2:Submitting Jobs|Find out how to submit computing jobs to the Hoffman2 Cluster.]]

==External Links==
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Webpage]
*[http://www.ats.ucla.edu/clusters/hoffman2/h2stat/statistics.htm Hoffman2 Statistics]
*[http://www.ats.ucla.edu/clusters/hosting/ Hoffman2 Cluster Hosting]
*[http://www.ats.ucla.edu/clusters/hoffman2/computing/batch/policies.htm Hoffman2 Queues]
*[http://www.ats.ucla.edu/clusters/hoffman2/hardware/default.htm Hoffman2 Hardware]
*[http://www.ats.ucla.edu/clusters/hoffman2/computing/gpuq.htm Hoffman2 GPU Cluster]
*[http://www.ats.ucla.edu/clusters/hoffman2/data_storage/default.htm Hoffman2 Data Storage]
*[http://www.ats.ucla.edu/clusters/hoffman2/computing/howtoscratch.htm Temporary File Storage for Fast I/O]

Hoffman2:Tools

2014-04-23T01:05:28Z

Ccn admin: Created page with "Back to all things Hoffman2 Helpful Tools/Hints Page! == Screens == This Unix tool lets you switch between multiple "screens" or terminal shells. One helpful tr..."

[[Hoffman2|Back to all things Hoffman2]]

Helpful Tools/Hints Page!

== Screens ==
This Unix tool lets you switch between multiple "screens" or terminal shells. One helpful trick is using screen to run your interactive sessions remotely.
:[[Using_Screen]]

Using Screen

2014-04-23T01:04:39Z

Ccn admin:

==What is Screen?==
From the [http://www.gnu.org/software/screen/ Gnu Screen] home page.

<blockquote>Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells. Each virtual terminal provides the functions of the DEC VT100 terminal and, in addition, several control functions from the ANSI X3.64 (ISO 6429) and ISO 2022 standards (e.g., insert/delete line and support for multiple character sets). There is a scrollback history buffer for each virtual terminal and a copy-and-paste mechanism that allows the user to move text regions between windows. When screen is called, it creates a single window with a shell in it (or the specified command) and then gets out of your way so that you can use the program as you normally would. Then, at any time, you can create new (full-screen) windows with other programs in them (including more shells), kill the current window, view a list of the active windows, turn output logging on and off, copy text between windows, view the scrollback history, switch between windows, etc. All windows run their programs completely independent of each other. Programs continue to run when their window is currently not visible and even when the whole screen session is detached from the users terminal.</blockquote>

==Quick Start==
Launch a QRSH (if on hoffman2) session:
$ qrsh -l h_data=4G
$ screen - Start Screen Session

Run bash/matlab script.

(While Computing :)
CTRL+A d - detach the screen session

$ screen -list - list all screen sessions. EXAMPLE OUTPUT 9368.ttyp1.cohen-static (Detached)

$ screen -r 9368 - Resume a screen session with an id of 9368 (see EXAMPLE above)

== Setup ==
First copy/paste the following configuration into a file and then save it as .screenrc in your Home directory (for osx users that's /Users/username/).

<code><pre>
# .screenrc
# Dave Kaufman
# http://davekaufman.net
#
# Created: 1 Jul 2002 04:00:00 PM EDT
# Last Modified: Sat 22 Jan 2005 11:41:18 PM EST
#
# This file is used to initialize screen sessions

# No annoying audible bell, using "visual bell"
#vbell on # default: off
#vbell_msg " -- Ring, Ring!! -- " # default: "Wuff,Wuff!!"

# Automatically detach on hangup.
autodetach on # default: on

# Don't display the copyright page
startup_message off # default: on

# Affects the copying of text regions
crlf off # default: off

# Change default scrollback value for new windows
defscrollback 1000 # default: 100

# Define the time that all windows monitored for silence should
# wait before displaying a message. Default 30 seconds.
silencewait 15

# Ensures that the default shell is the same as the value of the $SHELL env variable
shell -$SHELL

# emulate .logout message
pow_detach_msg "Screen session of \$LOGNAME \$:cr:\$:nl:ended."

# Pretty status bar at the bottom.
hardstatus alwayslastline
hardstatus string "%{gk}[ %{G}%H %{g}][%= %{wk}%?%-Lw%?%{r}(%{W}%n*%f %t%?(%u)%?%{r})%{w}%?%+Lw%?%?%= %{g}][%{B} %m/%d %{W}%c %{g}]"
# XTERM TWEAKS
# ===============================================================

# xterm understands both im/ic and doesn't have a status line.
# Note: Do not specify im and ic in the real termcap/info file as
# some programs (e.g. vi) will not work anymore.
termcap xterm hs@:cs=\E[%i%d;%dr:im=\E[4h:ei=\E[4l
terminfo xterm hs@:cs=\E[%i%p1%d;%p2%dr:im=\E[4h:ei=\E[4l

# 80/132 column switching must be enabled for ^AW to work
# change init sequence to not switch width
termcapinfo xterm Z0=\E[?3h:Z1=\E[?3l:is=\E[r\E[m\E[2J\E[H\E[?7h\E[?1;4;6l

# Make the output buffer large for (fast) xterms.
# termcapinfo xterm* OL=10000
termcapinfo xterm* OL=100

# tell screen that xterm can switch to dark background and has function
# keys.
termcapinfo xterm 'VR=\E[?5h:VN=\E[?5l'
termcapinfo xterm 'k1=\E[11~:k2=\E[12~:k3=\E[13~:k4=\E[14~'
termcapinfo xterm 'kh=\EOH:kI=\E[2~:kD=\E[3~:kH=\EOF:kP=\E[5~:kN=\E[6~'

# special xterm hardstatus: use the window title.
termcapinfo xterm 'hs:ts=\E]2;:fs=\007:ds=\E]2;screen\007'

#terminfo xterm 'vb=\E[?5h$<200/>\E[?5l'
termcapinfo xterm 'vi=\E[?25l:ve=\E[34h\E[?25h:vs=\E[34l'

# emulate part of the 'K' charset
termcapinfo xterm 'XC=K%,%\E(B,[\304,\\\\\326,]\334,{\344,|\366,}\374,~\337'

# xterm-52 tweaks:
# - uses background color for delete operations
termcapinfo xterm* be

# WYSE TERMINALS
# ===============================================================

#wyse-75-42 must have flow control (xo = "terminal uses xon/xoff")
#essential to have it here, as this is a slow terminal.
termcapinfo wy75-42 xo:hs@

# New termcap sequences for cursor application mode.
termcapinfo wy* CS=\E[?1h:CE=\E[?1l:vi=\E[?25l:ve=\E[?25h:VR=\E[?5h:VN=\E[?5l:cb=\E[1K:CD=\E[1J

# OTHER TERMINALS
# ===============================================================

# make hp700 termcap/info better
termcapinfo hp700 'Z0=\E[?3h:Z1=\E[?3l:hs:ts=\E[62"p\E[0$~\E[2$~\E[1$}:fs=\E[0}\E[61"p:ds=\E[62"p\E[1$~\E[61"p:ic@'

# Extend the vt100 desciption by some sequences.
termcap vt100* ms:AL=\E[%dL:DL=\E[%dM:UP=\E[%dA:DO=\E[%dB:LE=\E[%dD:RI=\E[%dC
terminfo vt100* ms:AL=\E[%p1%dL:DL=\E[%p1%dM:UP=\E[%p1%dA:DO=\E[%p1%dB:LE=\E[%p1%dD:RI=\E[%p1%dC
termcapinfo linux C8
# old rxvt versions also need this
# termcapinfo rxvt C8

# Change the escape key for hotkeys so I can run screen within screen
# escape ^l\\
# Let's remove some dangerous key bindings ...
bind k
bind ^k
bind .
bind ^\
bind \\
bind ^h
bind h

# ... and make them better.
bind 'K' kill
bind 'I' login on
bind 'O' login off
bind '}' history
bind 'Q' quit

# Yet another hack:
# Prepend/append register [/] to the paste if ^a^] is pressed.
# This lets me have autoindent mode in vi.
register [ "\033:se noai\015a"
register ] "\033:se ai\015a"
bind ^] paste [.]

# Resize the current region. The space will be removed from or added to
# the region below or if there's not enough space from the region above.
bind = resize =
bind + resize +3
bind - resize -3

# Time a message is displayed if screen is not disturbed by
# other activity. The dafault is 5 seconds:
msgwait 15

# change the default activity message to include a bell.
activity "Activity in %n ^G"

# Don't you want to start programs which need a DISPLAY ?
setenv DISPLAY ':0'

# Bind F11 and F12 (NOT F1 and F2) to previous and next screen window
bindkey -k F1 prev
bindkey -k F2 prev

# Default Buffers
screen -M -t Shell 0
screen -t Shell 1
screen -t Shell 2
screen -t Shell 3
select 0
</pre></code>

Then all that is left is to run it. Screen is included by default in every OSX package and is available in any package manager I've seen (ports, portage, rpm, etc). If your using OSX, just type the following at the command prompt:

$ screen

==No, not how do I start it. How do I use it?==
Ah, yeah, I suppose that would help. Here's a quick run down of the basics. After starting screen hit your space bar to exit out of the welcome screen. You'll see what looks like a normal run of the mill terminal session. If you copy/pasted the configuration file above you'll also see a very convenient bar at the bottom that tells you which screen window your currently in, how many you have, and the name of your computer.

All that is left is moving between these sessions, creating new ones, deleting old ones, and the holy grail of detaching and resuming sessions.

CTRL+A 1 - move to screen 1

CTRL+A 2 - move to screen 2

CTRL+A <num> - move to the screen with number <num>, e.g. 3, 4, 5, 6, <num>

CTRL+A X - move to screen X where X is a screen number

CTRL+A n - move to the (n)ext screen

CTRL+A c - (c)reate a new screen

$ exit - exit the current screen window (not the entire screen program, just that window)

CTRL+A d - detach the screen session

$ screen -list - list all screen sessions. EXAMPLE OUTPUT 9368.ttyp1.cohen-static (Detached)

$ screen -r 9368 - Resume a screen session with an id of 9368 (see EXAMPLE above)

==External Links==
*[http://www.kb.indiana.edu/data/acuy.html Indiana University UITS (additional information about screen)]
*[http://www.gnu.org/software/screen GNU Screen Homepage]

Hoffman2

2014-04-23T00:57:51Z

Ccn admin: /* Productivity */

A compilation of lab know-how regarding the Hoffman2 Computing Cluster.

Anyone new to the lab and using Hoffman2 NEEDS to read the first section to have adequate working knowledge of the system.

== Getting Started ==
=== Introduction ===
Hoffman2 is a Computing Cluster at UCLA, find out how it generally works so you know how to use it.
: [[Hoffman2:Introduction]]

=== Getting an Account ===
You know what it is, now you want to use it. First you need an account.
: [[Hoffman2:Getting an Account]]

=== Accessing the Cluster ===
Now how do you use that account to access the cluster?
: [[Hoffman2:Accessing the Cluster]]

=== Working in a UNIX Environment ===
Never heard of a command line before today? Vaguely know what "permissions" are and have no idea how to navigate a filesystem? This page is meant to take the scary out of the words "command line" so you can actually use Hoffman2, because no matter how many GUIs there are you will still need to command line sometimes.
: [[Hoffman2:UNIX Tutorial]]

=== Quotas ===
Resources are not infinite, and disk space is a resource. Find out how to manage your disk space usage to stay under quota.
: [[Hoffman2:Quotas]]

=== Profile ===
You have an account, know how to get there, and now you need to make one last step for you account to be fully usable.
: [[Hoffman2:Profile]]

== Computing ==
You can find your way through Hoffman2, now it is time to start making things happen.

=== Software Tools ===
You've got your account, you are logged on, now how do you get to using a real software tool?
: [[Hoffman2:Software Tools]]

=== Submitting Jobs ===
Now you have the tools, but how does one ask Hoffman2 to run them for you as a job? Since you aren't supposed to be running them on a login node...
: [[Hoffman2:Submitting Jobs]]

=== Monitoring Jobs ===
Right after they zap their monster to life, every mad scientist wishes they had the tools to check on or stop their creation. Now that you can submit jobs, you need to be able to check on them and stop them if they start terrorizing downtown Tokyo.
: [[Hoffman2:Monitoring Jobs]]

=== Interactive Sessions ===
Some software tools need you to interact with them while they work. Other times you just need to be able to run your script over and over while you work to eradicate all of its bugs. Enter ''Interactive'' Sessions.
: [[Hoffman2:Interactive Sessions]]

== Software ==
=== MATLAB ===
How to use MATLAB on the cluster. It is easier than you think.
: [[Hoffman2:MATLAB]]

==== Compiling MATLAB ====
So you have a MATLAB script, but you don't need to GUI open all night to have it process your data. How to submit MATLAB jobs to Hoffman2.
: [[Hoffman2:Compiling MATLAB]]

==== EEGLAB ====
We try to maintain the three most recent versions of EEGLAB for your convenience. Make sure to add it to your MATLAB path.
: [[Hoffman2:MATLAB:EEGLAB]]

===== EEGLAB Jobs =====
Processing multiple subjects through EEGLAB can be tiring and inconvenient if you do it by hand. Learn how to make scripts that run as jobs leveraging the power of Hoffman2.
: [[Hoffman2:MATLAB:EEGLAB:Jobs]]

==== SPM Compiled (Batch) ====
Maybe FSL isn't your cup of tea for neuroimaging work. SPM is a capable alternative and, even though it is MATLAB based, it has a compiled version that will let you leverage the power of the cluster.
: [[Hoffman2:MATLAB:SPM]]

=== R ===
You are probably a statistician, or you just prefer open source software. Here's how to run R on Hoffman2.
: [[Hoffman2:R]]

=== WEKA ===
If machine learning is your thing, maybe you've heard of WEKA. If not, maybe it will be your new best friend.
: [[Hoffman2:WEKA]]

=== LONI Pipeline ===
A Workflow application to make things easier.
: [[Hoffman2:LONI]]

=== FSL ===
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
: [[Hoffman2:FSL]]

== Productivity ==
How about streamlining some of those tasks, or getting more things done.

=== Scripts ===
All of the difficulties you are experiencing now have probably been experienced before by someone else. And for that reason we already have scripts to simplify your life.
: [[Hoffman2:Scripts]]

=== Data Transfer ===
All dressed up with no where to go? That's how Hoffman2 feels if you don't give it any data to work with. Find out how to avoid hurting the Cluster's feelings.
: [[Hoffman2:Data Transfer]]

=== Sharing Filesystems ===
All you want to do is be able to look at your precious data. But it is locked up on Hoffman2 and you want to use tools on your computer to look at it. There's an app for that.
: [[Hoffman2:Sharing Filesystems]]

=== Tools ===
Simple tools that will help your productivity.
: [[Hoffman2:Tools]]

== FAQ ==
Wesley's Usage, so you can plan around it and ask him to stop beating the cluster up.
: [[Hoffman2:WTK Usage]]

Unfolding

2014-01-28T01:55:16Z

Ccn admin: /* Directory Outline: How to Open FSLView Through Terminal */

There are several steps to successfully unfolding the high resolution scans of the hippocampus. The details for this section fall into the broad categories of segmentation, interpolation, demarcations, and calculating thickness. A knowledge of command line is necessary, as well as obtaining the tools for each step.

==Tools Required==
*A copy of Windows
*A virtual machine emulator
*A command line interface to connect to [[Hoffman2|hoffman]]
*MrGray (Windows only)
*Matlab

==Segmentation==
===Overview===
The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

===Getting Started: The Initial Segmentation Checklist===
#Export all of your vAnatomyCrop.dat files to a PC (ftp using binary).
#Run the program mrGray
#Create a new project and name it after your subject. Use the following nomenclature:
::AD_#####
:::ex. AD_12345

For a subject with the Small ID 12345, who was scanned on May 25th, 2012, the following would be the subject entry in /u/home/data/sbook/data/AD/subjects:
::subj ID: AD_12345
::date: 20120525 (yyyymmdd)
::And it would be in the following path:
:::/u/home/sbook/data/AD/subjects/AD_12345/20120525/... etc etc.

Subjects file names should look like:
::subject ID: AD_12345
::subject scan date: 20120525
::segmentation: AD_12345_seg
::interpolation: AD_12345_interpright or AD_12345_interpleft

Once you have completed the segmentation session make sure to update our filemaker tab in objective fitness spreadsheet
::Select name for new project in AD/subjects/AD_XXXXX/SCANDATE/analysis/structural/unfold/segmentation
:::Select vAnatomyCrop.dat
:::Figure out which slices to segment based on anatomical guidelines.
::::*Anteriorly, choosing the last slice in which hippocampal head is visible is a consistent start point we've used

::Below are anatomical diagrams of the hippocampus and what to look for:
[[File:unfolding-Anat.png]]
:::Figure 1. Anatomical diagram, with an inferior view of the whole brain at the left, an inferior view of the temporal lobe at the center, and coronal sections from the two indicated slices at the right. A: Anterior slice through entorhinal cortex. B: Posterior slice through parahippocampal cortex. ERC, entorhinal cortex; PRC, perirhinal cortex; PHC, parahippocampal cortex; FG, fusiform gyrus; Sub, subiculum; CA 1,cornu ammonis 1; CA 2,3, CA fields 2 and 3; DG, dentate gyrus; CoS, collateral sulcus.
[[File:unfolding-Hipp.png]]
:::Figure 2. Coronal view of right side of the hippocampus. In the coronal plane the hippocampus and parahippocampal gyrus form an S-shaped configuration. The hippocampus itself consists of two interlocking C-shaped structures: the cornu ammonis and the dentate gyrus. Histologically, the hippocampus is further divided into 4 sections CA1 to CA4.

Once file is created, you may begin segmentation process:
#Segment the white matter 1st (colored in beige) (red in our lab), using a pixel size of 3 pixels minimum
#Select white matter with the checkbox at the right
#Another checkbox indicates the highlight size (use 3)
#The left mouse button highlights a pixel, and the right mouse button deselects pixels
#Then, segment the CSF (colored in yellow) (blue in our lab), imposing a thin boundary on the segmentation. (You want it thin because you will expand it after the interpolation step).
#Save the segmentation (File -> Classification -> Save as with the above nomenclature).
::*'''Save early, save often.'''

Here is an example of an initial segmentation: Starting anteriorly and ending posteriorly:

:[[File:unfolding-Seg_P1.png]]
:[[File:unfolding-Seg_P2.png]]

==Interpolation==
Explain [[interpolation]] here.

To load an existing project, when you're in MrGray, you'll click on Load project and you can select any .mrp file.
These will be named AD_1XXXX_interpleft or _interpright. It will then appear and you should be able to see the CSF
and white matter masks if they are selected in the toolbar.

Create a new interpolation file; these are the steps you will take:

# Open the menu and select File > New Project
# In the first window go to the subject's unfold directory (ie. ...AD/subjects/AD_1XXXX/2012####/analysis/structural/unfold/interpolation)
# Name the project AD_1XXXX_interpleft or AD_1XXXX_interpright and hit enter
# In the second window select the Volume anatomy file for the interpolation file (vAnatInterp.dat file) and hit enter
# When the image displays, you will now go to the File menu again and then to "Classification". Then click "load classification file".
# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.
# Check to make sure the masks align correctly.

==Demarcations==

===Getting Started===
After segmentation and interpolation, [[demarcations]] create the boundaries for the different region of the hippocampus. These boundaries can be conveniently drawn using FSLview. Open your hire structural image. Be sure this is the same brain that you used for the unfolding process. It is important to note that these images are in radiological convention, so if you're drawing on the right side of the screen, this is actually the left hemisphere. Look at your notes to determine which slices were segmented and used for unfolding; only draw boundaries on the slices that have been segmented. To create a new boundary, go to the file menu and select "Create Mask." In the lower left corner, you'll see a blue "i"; click on this to re-name your boundary as needed, and to select the color you'd like to draw with. To zoom in on the MTL, first go to View/Single, and then expland the coronal image. Use the zoom tool to magnify the MTL. Click on the pencil tool, and make adjustments as desired. A brightness with typically a max of 1 and a small pencil size work best. If using a mouse, the left button draws the boundary and the ctrl+ left button erases. When saving, be sure to save to your Demarcations directory, and to use the proper naming convention. It is best to complete one boundary at a time across all slices, and then move on to the next boundary.

===General Tips===
Before starting to draw, you want to first identify the slice where the hippocampal head begins. It is important to note that where the hippocampal head "begins" means where it begins when going in the Posterior to Anterior direction. This slice, which will be called the '''hippocampal head slice''' throughout the rest of these instructions is where the anterior structures will start. Also, drawing shorter/smaller boundaries will reduce variability once projected onto the flat maps, giving you a straighter line. In general, boundary doesn't need to cross the entire gray matter area; keep the boundary towards the medial or superior side of things, as appropriate.

===Naming Convention===
Boundaries drawn on all the slices:
*'''Fus'''(Fusiform)
* '''CollSul'''(Collateral Sulcus)
*'''SubCA1'''(Subiculum-CA1)
* '''CA1CA23DG'''(CA1-CA23DG)
Boundaries drawn on anterior slices only:
*'''ERCSub''' (Entorhinal Coral- Subiculum)
*'''PRCERC''' (Perirhinal Cortex- Entorhinal Cortex)
*'''AntCADG''' (Anterior portion of CA fields and Dentate Gyrus)
* '''ERCPRCPHC''' (Boundary between anterior structures Entorhinal/Perirhinal Cortices and the posterior structure Parahippocampal Cortex)
Boundaries drawn on the posterior slices only:
*'''PHCSub''' (Parahippocampal Cortex- Subiculum)

===Individual Boundaries===
On each of the slices that were segmented, we must determine which boundaries to mark.

'''Fusiform (Fus)'''
::[[File:unfolding-Fus.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the lateral side of the collateral sulcus (on the side closer to the second sulcus)
::*Outline of collateral sulcul shown in red; boundary between sulcus and fusiform gyrus shown in yellow
::*Fusiform is lateral to the boundary
'''Collateral Sulcus (CollSul)'''
::[[File:unfolding-CollSul.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend in the superior tip of the collateral sulcus
::*Outline of collateral sulcus shown in yellow; boundary shown in red
'''Separating PHC from Subiculum (PHCSub)'''
::[[File:unfolding-PHCSub.jpg]]
::*Posterior slices only
::*Begin drawing on the first slice posterior to the hippocampal head slice, and continue to draw on the remainder of the posterior slices
::*Draw boundary perpendicular to the gray matter ribbon approximately 50% of the way up the bend
::*Bend shown in red, boundary between subiculum and PHC shown in green
::*Subiculum is superior to boundary
'''Separating Subiculum from CA1 (SubCA1)'''
::*Both anterior and posterior slices
::*''Anterior'': boundary more lateral; draw boundary underneath "bump" where the curve of the hippocampus comes in, bisecting it
:::* Bump shown in red, boundary between Sub and CA1 shown in blue
:::* Sub is medial to the boundary, CA1 is lateral
::: [[File:unfolding-SubCA1_Anterior.jpg]]
::*''Posterior'': boundary more medial; draw boundary where the hippocampus pinches off into a tear-drop shape, or folds into itself
:::*Teardrop shown in red, boundary between Sub and CA1 shown in blue
:::*Sub is medial to the boundary, CA1 is lateral
:::[[File:unfolding-SubCA1_Posterior.jpg]]
'''Separating CA1 from CA23DG (CA1CA23DG)'''
::[[File:unfolding-CA1CA23DG.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend (on the path where the hippocampal fissure would extend to in the hippocampal head)
::*Bend shown in red; boundary between CA1CA23DG shown in green
'''Separating ERC from Subiculum (ERCSub)'''
::[[File:unfolding-ERCSub.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*If you were to continue the lateral boundary of the hippocampus inwards medially, it would divide the hippocampus and the ERC
::*Draw boundary along this divide, perpendicular to gray matter ribbon
::*Lateral boundary shown in red, boundary between ERC and Sub shown in yellow
'''Separating PRC from ERC (PRCERC)'''
::[[File:unfolding-PRCERC.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the medial side of the collateral sulcus (the side of the collateral sulcus closer to the hippocampal head)
::*Collateral sulcus outlined in yellow, boundary between PRC and ERC in green
::*ERC medial to boundary, PRC lateral
'''Anterior CA fields and Dentate Gyrus (AntCADG)'''
::[[File:unfolding-AntCADG.jpg]]
::*Only one slice: draw on the first slice anterior to the hippocampal head slice (this should be the slice where you first see undulations going in the Posterior to Anterior direction)
::*Draw boundary straight through middle of CADG area, and extend all the way laterally to the CA1CA23DG boundary (go through the middle of the hippocampal head between the fissure and the top of the head)
::*Undulations highlighted in red; CA1CA23DG boundary in green; AntCADG boundary in white
'''Creating A/P boundary (ERCPRCPHC)'''
::[[File:unfolding-ERCPRCPHC.jpg]]
::*Only one slice: draw on the hippocampal head slice
::*Starting at the ERCSub boundary, draw a line in the middle of the gray matter ribbon up and over the collateral sulcus, all the way out to the Fus boundary
::* ERCSub and Fus boundaries shown in yellow
::* ERCPRCPHC boundary shown in white

===Directory Outline: How to Open FSLView Through Terminal===
:Below is an outline for the directory path. In order to open files for segmentation, interpolation, and demarcation in the unfolding process, you must be able to navigate the Terminal.

::[[File:unfolding-Dir_Route.png]]

The best way to open FSLview in order to do demarcations is through the FSLview path in ''Terminal''. Below are the following steps to open a file for demarcations.

#ssh -X johnsmith@hoffman2.idre.ucla.edu
: This is your login. You must have a '''hoffman''' account to access ''Terminal''
#/u/home/FMRI/sbook/data/AD/subjects
: This is your homebase directory. Once logged into hoffman, you will be able to access the path of directories seen above.
::For each subject, there is a '''nii''' directory and a '''analysis''' directory, which contain information used for demarcations.
:::The '''nii''' directory contains the image files for the brain scans.
:::The '''analysis''' directory contains the subdirectories '''preprocessing''' and '''structural'''.
::::The preprocessing directory may also contain the hhr structural image file, as seen in the nii directory .
::::The structural directory contains the '''unfold''' directory which contains folders for ''segmentation'', ''interpolation'', and ''demarcations''.
#cd AD_10210/2008XXXX/analysis/structural/unfold
:In this unfold directory, you can check if the hhr image file is already in preprocessing. If the hhr image file is already in the preprocessing directory, it can be opened directly in FSL view.
#fslview hhr_struct_6.nii.gz
: If the hhr image is not in the preprocessing directory, you can copy the image from the '''nii''' directory into the '''preprocessing''' and then open it in FSL view.
#cd ../../../subjects/AD_1XXXXX
#cd nii
#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz
##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)

==External Links==
*[https://www.virtualbox.org/ Virtual Box: Virtual machine software]
*[http://white.stanford.edu/~brian/mri/segmentUnfold.htm MrGray Segmentation software for Windows]
*[http://www.cygwin.com/ Cygwin Command-line interface for Windows]
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Home Page]

Unfolding

2014-01-28T01:54:39Z

Ccn admin: /* Individual Boundaries */

There are several steps to successfully unfolding the high resolution scans of the hippocampus. The details for this section fall into the broad categories of segmentation, interpolation, demarcations, and calculating thickness. A knowledge of command line is necessary, as well as obtaining the tools for each step.

==Tools Required==
*A copy of Windows
*A virtual machine emulator
*A command line interface to connect to [[Hoffman2|hoffman]]
*MrGray (Windows only)
*Matlab

==Segmentation==
===Overview===
The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

===Getting Started: The Initial Segmentation Checklist===
#Export all of your vAnatomyCrop.dat files to a PC (ftp using binary).
#Run the program mrGray
#Create a new project and name it after your subject. Use the following nomenclature:
::AD_#####
:::ex. AD_12345

For a subject with the Small ID 12345, who was scanned on May 25th, 2012, the following would be the subject entry in /u/home/data/sbook/data/AD/subjects:
::subj ID: AD_12345
::date: 20120525 (yyyymmdd)
::And it would be in the following path:
:::/u/home/sbook/data/AD/subjects/AD_12345/20120525/... etc etc.

Subjects file names should look like:
::subject ID: AD_12345
::subject scan date: 20120525
::segmentation: AD_12345_seg
::interpolation: AD_12345_interpright or AD_12345_interpleft

Once you have completed the segmentation session make sure to update our filemaker tab in objective fitness spreadsheet
::Select name for new project in AD/subjects/AD_XXXXX/SCANDATE/analysis/structural/unfold/segmentation
:::Select vAnatomyCrop.dat
:::Figure out which slices to segment based on anatomical guidelines.
::::*Anteriorly, choosing the last slice in which hippocampal head is visible is a consistent start point we've used

::Below are anatomical diagrams of the hippocampus and what to look for:
[[File:unfolding-Anat.png]]
:::Figure 1. Anatomical diagram, with an inferior view of the whole brain at the left, an inferior view of the temporal lobe at the center, and coronal sections from the two indicated slices at the right. A: Anterior slice through entorhinal cortex. B: Posterior slice through parahippocampal cortex. ERC, entorhinal cortex; PRC, perirhinal cortex; PHC, parahippocampal cortex; FG, fusiform gyrus; Sub, subiculum; CA 1,cornu ammonis 1; CA 2,3, CA fields 2 and 3; DG, dentate gyrus; CoS, collateral sulcus.
[[File:unfolding-Hipp.png]]
:::Figure 2. Coronal view of right side of the hippocampus. In the coronal plane the hippocampus and parahippocampal gyrus form an S-shaped configuration. The hippocampus itself consists of two interlocking C-shaped structures: the cornu ammonis and the dentate gyrus. Histologically, the hippocampus is further divided into 4 sections CA1 to CA4.

Once file is created, you may begin segmentation process:
#Segment the white matter 1st (colored in beige) (red in our lab), using a pixel size of 3 pixels minimum
#Select white matter with the checkbox at the right
#Another checkbox indicates the highlight size (use 3)
#The left mouse button highlights a pixel, and the right mouse button deselects pixels
#Then, segment the CSF (colored in yellow) (blue in our lab), imposing a thin boundary on the segmentation. (You want it thin because you will expand it after the interpolation step).
#Save the segmentation (File -> Classification -> Save as with the above nomenclature).
::*'''Save early, save often.'''

Here is an example of an initial segmentation: Starting anteriorly and ending posteriorly:

:[[File:unfolding-Seg_P1.png]]
:[[File:unfolding-Seg_P2.png]]

==Interpolation==
Explain [[interpolation]] here.

To load an existing project, when you're in MrGray, you'll click on Load project and you can select any .mrp file.
These will be named AD_1XXXX_interpleft or _interpright. It will then appear and you should be able to see the CSF
and white matter masks if they are selected in the toolbar.

Create a new interpolation file; these are the steps you will take:

# Open the menu and select File > New Project
# In the first window go to the subject's unfold directory (ie. ...AD/subjects/AD_1XXXX/2012####/analysis/structural/unfold/interpolation)
# Name the project AD_1XXXX_interpleft or AD_1XXXX_interpright and hit enter
# In the second window select the Volume anatomy file for the interpolation file (vAnatInterp.dat file) and hit enter
# When the image displays, you will now go to the File menu again and then to "Classification". Then click "load classification file".
# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.
# Check to make sure the masks align correctly.

==Demarcations==

===Getting Started===
After segmentation and interpolation, [[demarcations]] create the boundaries for the different region of the hippocampus. These boundaries can be conveniently drawn using FSLview. Open your hire structural image. Be sure this is the same brain that you used for the unfolding process. It is important to note that these images are in radiological convention, so if you're drawing on the right side of the screen, this is actually the left hemisphere. Look at your notes to determine which slices were segmented and used for unfolding; only draw boundaries on the slices that have been segmented. To create a new boundary, go to the file menu and select "Create Mask." In the lower left corner, you'll see a blue "i"; click on this to re-name your boundary as needed, and to select the color you'd like to draw with. To zoom in on the MTL, first go to View/Single, and then expland the coronal image. Use the zoom tool to magnify the MTL. Click on the pencil tool, and make adjustments as desired. A brightness with typically a max of 1 and a small pencil size work best. If using a mouse, the left button draws the boundary and the ctrl+ left button erases. When saving, be sure to save to your Demarcations directory, and to use the proper naming convention. It is best to complete one boundary at a time across all slices, and then move on to the next boundary.

===General Tips===
Before starting to draw, you want to first identify the slice where the hippocampal head begins. It is important to note that where the hippocampal head "begins" means where it begins when going in the Posterior to Anterior direction. This slice, which will be called the '''hippocampal head slice''' throughout the rest of these instructions is where the anterior structures will start. Also, drawing shorter/smaller boundaries will reduce variability once projected onto the flat maps, giving you a straighter line. In general, boundary doesn't need to cross the entire gray matter area; keep the boundary towards the medial or superior side of things, as appropriate.

===Naming Convention===
Boundaries drawn on all the slices:
*'''Fus'''(Fusiform)
* '''CollSul'''(Collateral Sulcus)
*'''SubCA1'''(Subiculum-CA1)
* '''CA1CA23DG'''(CA1-CA23DG)
Boundaries drawn on anterior slices only:
*'''ERCSub''' (Entorhinal Coral- Subiculum)
*'''PRCERC''' (Perirhinal Cortex- Entorhinal Cortex)
*'''AntCADG''' (Anterior portion of CA fields and Dentate Gyrus)
* '''ERCPRCPHC''' (Boundary between anterior structures Entorhinal/Perirhinal Cortices and the posterior structure Parahippocampal Cortex)
Boundaries drawn on the posterior slices only:
*'''PHCSub''' (Parahippocampal Cortex- Subiculum)

===Individual Boundaries===
On each of the slices that were segmented, we must determine which boundaries to mark.

'''Fusiform (Fus)'''
::[[File:unfolding-Fus.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the lateral side of the collateral sulcus (on the side closer to the second sulcus)
::*Outline of collateral sulcul shown in red; boundary between sulcus and fusiform gyrus shown in yellow
::*Fusiform is lateral to the boundary
'''Collateral Sulcus (CollSul)'''
::[[File:unfolding-CollSul.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend in the superior tip of the collateral sulcus
::*Outline of collateral sulcus shown in yellow; boundary shown in red
'''Separating PHC from Subiculum (PHCSub)'''
::[[File:unfolding-PHCSub.jpg]]
::*Posterior slices only
::*Begin drawing on the first slice posterior to the hippocampal head slice, and continue to draw on the remainder of the posterior slices
::*Draw boundary perpendicular to the gray matter ribbon approximately 50% of the way up the bend
::*Bend shown in red, boundary between subiculum and PHC shown in green
::*Subiculum is superior to boundary
'''Separating Subiculum from CA1 (SubCA1)'''
::*Both anterior and posterior slices
::*''Anterior'': boundary more lateral; draw boundary underneath "bump" where the curve of the hippocampus comes in, bisecting it
:::* Bump shown in red, boundary between Sub and CA1 shown in blue
:::* Sub is medial to the boundary, CA1 is lateral
::: [[File:unfolding-SubCA1_Anterior.jpg]]
::*''Posterior'': boundary more medial; draw boundary where the hippocampus pinches off into a tear-drop shape, or folds into itself
:::*Teardrop shown in red, boundary between Sub and CA1 shown in blue
:::*Sub is medial to the boundary, CA1 is lateral
:::[[File:unfolding-SubCA1_Posterior.jpg]]
'''Separating CA1 from CA23DG (CA1CA23DG)'''
::[[File:unfolding-CA1CA23DG.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend (on the path where the hippocampal fissure would extend to in the hippocampal head)
::*Bend shown in red; boundary between CA1CA23DG shown in green
'''Separating ERC from Subiculum (ERCSub)'''
::[[File:unfolding-ERCSub.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*If you were to continue the lateral boundary of the hippocampus inwards medially, it would divide the hippocampus and the ERC
::*Draw boundary along this divide, perpendicular to gray matter ribbon
::*Lateral boundary shown in red, boundary between ERC and Sub shown in yellow
'''Separating PRC from ERC (PRCERC)'''
::[[File:unfolding-PRCERC.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the medial side of the collateral sulcus (the side of the collateral sulcus closer to the hippocampal head)
::*Collateral sulcus outlined in yellow, boundary between PRC and ERC in green
::*ERC medial to boundary, PRC lateral
'''Anterior CA fields and Dentate Gyrus (AntCADG)'''
::[[File:unfolding-AntCADG.jpg]]
::*Only one slice: draw on the first slice anterior to the hippocampal head slice (this should be the slice where you first see undulations going in the Posterior to Anterior direction)
::*Draw boundary straight through middle of CADG area, and extend all the way laterally to the CA1CA23DG boundary (go through the middle of the hippocampal head between the fissure and the top of the head)
::*Undulations highlighted in red; CA1CA23DG boundary in green; AntCADG boundary in white
'''Creating A/P boundary (ERCPRCPHC)'''
::[[File:unfolding-ERCPRCPHC.jpg]]
::*Only one slice: draw on the hippocampal head slice
::*Starting at the ERCSub boundary, draw a line in the middle of the gray matter ribbon up and over the collateral sulcus, all the way out to the Fus boundary
::* ERCSub and Fus boundaries shown in yellow
::* ERCPRCPHC boundary shown in white

===Directory Outline: How to Open FSLView Through Terminal===
:Below is an outline for the directory path. In order to open files for segmentation, interpolation, and demarcation in the unfolding process, you must be able to navigate the Terminal.

::[[File:unfolding-directory_route.png]]

The best way to open FSLview in order to do demarcations is through the FSLview path in ''Terminal''. Below are the following steps to open a file for demarcations.

#ssh -X johnsmith@hoffman2.idre.ucla.edu
: This is your login. You must have a '''hoffman''' account to access ''Terminal''
#/u/home/FMRI/sbook/data/AD/subjects
: This is your homebase directory. Once logged into hoffman, you will be able to access the path of directories seen above.
::For each subject, there is a '''nii''' directory and a '''analysis''' directory, which contain information used for demarcations.
:::The '''nii''' directory contains the image files for the brain scans.
:::The '''analysis''' directory contains the subdirectories '''preprocessing''' and '''structural'''.
::::The preprocessing directory may also contain the hhr structural image file, as seen in the nii directory .
::::The structural directory contains the '''unfold''' directory which contains folders for ''segmentation'', ''interpolation'', and ''demarcations''.
#cd AD_10210/2008XXXX/analysis/structural/unfold
:In this unfold directory, you can check if the hhr image file is already in preprocessing. If the hhr image file is already in the preprocessing directory, it can be opened directly in FSL view.
#fslview hhr_struct_6.nii.gz
: If the hhr image is not in the preprocessing directory, you can copy the image from the '''nii''' directory into the '''preprocessing''' and then open it in FSL view.
#cd ../../../subjects/AD_1XXXXX
#cd nii
#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz
##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)

==External Links==
*[https://www.virtualbox.org/ Virtual Box: Virtual machine software]
*[http://white.stanford.edu/~brian/mri/segmentUnfold.htm MrGray Segmentation software for Windows]
*[http://www.cygwin.com/ Cygwin Command-line interface for Windows]
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Home Page]

File:Unfolding-Dir Route.png

2014-01-28T01:53:53Z

Ccn admin:

File:Unfolding-ERCPRCPHC.jpg

2014-01-28T01:53:22Z

Ccn admin:

File:Unfolding-AntCADG.jpg

2014-01-28T01:52:13Z

Ccn admin:

File:Unfolding-PRCERC.jpg

2014-01-28T01:51:53Z

Ccn admin:

File:Unfolding-ERCSub.jpg

2014-01-28T01:51:30Z

Ccn admin:

File:Unfolding-CA1CA23DG.jpg

2014-01-28T01:50:35Z

Ccn admin:

File:Unfolding-PHCSub.jpg

2014-01-28T01:50:01Z

Ccn admin:

File:Unfolding-CollSul.jpg

2014-01-28T01:49:58Z

Ccn admin:

File:Unfolding-SubCA1 Posterior.jpg

2014-01-28T01:49:54Z

Ccn admin:

File:Unfolding-SubCA1 Anterior.jpg

2014-01-28T01:49:47Z

Ccn admin:

File:Unfolding-Fus.jpg

2014-01-28T01:47:51Z

Ccn admin:

Unfolding

2014-01-28T01:44:57Z

Ccn admin:

There are several steps to successfully unfolding the high resolution scans of the hippocampus. The details for this section fall into the broad categories of segmentation, interpolation, demarcations, and calculating thickness. A knowledge of command line is necessary, as well as obtaining the tools for each step.

==Tools Required==
*A copy of Windows
*A virtual machine emulator
*A command line interface to connect to [[Hoffman2|hoffman]]
*MrGray (Windows only)
*Matlab

==Segmentation==
===Overview===
The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

===Getting Started: The Initial Segmentation Checklist===
#Export all of your vAnatomyCrop.dat files to a PC (ftp using binary).
#Run the program mrGray
#Create a new project and name it after your subject. Use the following nomenclature:
::AD_#####
:::ex. AD_12345

For a subject with the Small ID 12345, who was scanned on May 25th, 2012, the following would be the subject entry in /u/home/data/sbook/data/AD/subjects:
::subj ID: AD_12345
::date: 20120525 (yyyymmdd)
::And it would be in the following path:
:::/u/home/sbook/data/AD/subjects/AD_12345/20120525/... etc etc.

Subjects file names should look like:
::subject ID: AD_12345
::subject scan date: 20120525
::segmentation: AD_12345_seg
::interpolation: AD_12345_interpright or AD_12345_interpleft

Once you have completed the segmentation session make sure to update our filemaker tab in objective fitness spreadsheet
::Select name for new project in AD/subjects/AD_XXXXX/SCANDATE/analysis/structural/unfold/segmentation
:::Select vAnatomyCrop.dat
:::Figure out which slices to segment based on anatomical guidelines.
::::*Anteriorly, choosing the last slice in which hippocampal head is visible is a consistent start point we've used

::Below are anatomical diagrams of the hippocampus and what to look for:
[[File:unfolding-Anat.png]]
:::Figure 1. Anatomical diagram, with an inferior view of the whole brain at the left, an inferior view of the temporal lobe at the center, and coronal sections from the two indicated slices at the right. A: Anterior slice through entorhinal cortex. B: Posterior slice through parahippocampal cortex. ERC, entorhinal cortex; PRC, perirhinal cortex; PHC, parahippocampal cortex; FG, fusiform gyrus; Sub, subiculum; CA 1,cornu ammonis 1; CA 2,3, CA fields 2 and 3; DG, dentate gyrus; CoS, collateral sulcus.
[[File:unfolding-Hipp.png]]
:::Figure 2. Coronal view of right side of the hippocampus. In the coronal plane the hippocampus and parahippocampal gyrus form an S-shaped configuration. The hippocampus itself consists of two interlocking C-shaped structures: the cornu ammonis and the dentate gyrus. Histologically, the hippocampus is further divided into 4 sections CA1 to CA4.

Once file is created, you may begin segmentation process:
#Segment the white matter 1st (colored in beige) (red in our lab), using a pixel size of 3 pixels minimum
#Select white matter with the checkbox at the right
#Another checkbox indicates the highlight size (use 3)
#The left mouse button highlights a pixel, and the right mouse button deselects pixels
#Then, segment the CSF (colored in yellow) (blue in our lab), imposing a thin boundary on the segmentation. (You want it thin because you will expand it after the interpolation step).
#Save the segmentation (File -> Classification -> Save as with the above nomenclature).
::*'''Save early, save often.'''

Here is an example of an initial segmentation: Starting anteriorly and ending posteriorly:

:[[File:unfolding-Seg_P1.png]]
:[[File:unfolding-Seg_P2.png]]

==Interpolation==
Explain [[interpolation]] here.

To load an existing project, when you're in MrGray, you'll click on Load project and you can select any .mrp file.
These will be named AD_1XXXX_interpleft or _interpright. It will then appear and you should be able to see the CSF
and white matter masks if they are selected in the toolbar.

Create a new interpolation file; these are the steps you will take:

# Open the menu and select File > New Project
# In the first window go to the subject's unfold directory (ie. ...AD/subjects/AD_1XXXX/2012####/analysis/structural/unfold/interpolation)
# Name the project AD_1XXXX_interpleft or AD_1XXXX_interpright and hit enter
# In the second window select the Volume anatomy file for the interpolation file (vAnatInterp.dat file) and hit enter
# When the image displays, you will now go to the File menu again and then to "Classification". Then click "load classification file".
# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.
# Check to make sure the masks align correctly.

==Demarcations==

===Getting Started===
After segmentation and interpolation, [[demarcations]] create the boundaries for the different region of the hippocampus. These boundaries can be conveniently drawn using FSLview. Open your hire structural image. Be sure this is the same brain that you used for the unfolding process. It is important to note that these images are in radiological convention, so if you're drawing on the right side of the screen, this is actually the left hemisphere. Look at your notes to determine which slices were segmented and used for unfolding; only draw boundaries on the slices that have been segmented. To create a new boundary, go to the file menu and select "Create Mask." In the lower left corner, you'll see a blue "i"; click on this to re-name your boundary as needed, and to select the color you'd like to draw with. To zoom in on the MTL, first go to View/Single, and then expland the coronal image. Use the zoom tool to magnify the MTL. Click on the pencil tool, and make adjustments as desired. A brightness with typically a max of 1 and a small pencil size work best. If using a mouse, the left button draws the boundary and the ctrl+ left button erases. When saving, be sure to save to your Demarcations directory, and to use the proper naming convention. It is best to complete one boundary at a time across all slices, and then move on to the next boundary.

===General Tips===
Before starting to draw, you want to first identify the slice where the hippocampal head begins. It is important to note that where the hippocampal head "begins" means where it begins when going in the Posterior to Anterior direction. This slice, which will be called the '''hippocampal head slice''' throughout the rest of these instructions is where the anterior structures will start. Also, drawing shorter/smaller boundaries will reduce variability once projected onto the flat maps, giving you a straighter line. In general, boundary doesn't need to cross the entire gray matter area; keep the boundary towards the medial or superior side of things, as appropriate.

===Naming Convention===
Boundaries drawn on all the slices:
*'''Fus'''(Fusiform)
* '''CollSul'''(Collateral Sulcus)
*'''SubCA1'''(Subiculum-CA1)
* '''CA1CA23DG'''(CA1-CA23DG)
Boundaries drawn on anterior slices only:
*'''ERCSub''' (Entorhinal Coral- Subiculum)
*'''PRCERC''' (Perirhinal Cortex- Entorhinal Cortex)
*'''AntCADG''' (Anterior portion of CA fields and Dentate Gyrus)
* '''ERCPRCPHC''' (Boundary between anterior structures Entorhinal/Perirhinal Cortices and the posterior structure Parahippocampal Cortex)
Boundaries drawn on the posterior slices only:
*'''PHCSub''' (Parahippocampal Cortex- Subiculum)

===Individual Boundaries===
On each of the slices that were segmented, we must determine which boundaries to mark.

'''Fusiform (Fus)'''
::[[File:unfolding-Fus.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the lateral side of the collateral sulcus (on the side closer to the second sulcus)
::*Outline of collateral sulcul shown in red; boundary between sulcus and fusiform gyrus shown in yellow
::*Fusiform is lateral to the boundary
'''Collateral Sulcus (CollSul)'''
::[[File:unfolding-CollSul.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend in the superior tip of the collateral sulcus
::*Outline of collateral sulcus shown in yellow; boundary shown in red
'''Separating PHC from Subiculum (PHCSub)'''
::[[File:unfolding-PHCSub.jpg]]
::*Posterior slices only
::*Begin drawing on the first slice posterior to the hippocampal head slice, and continue to draw on the remainder of the posterior slices
::*Draw boundary perpendicular to the gray matter ribbon approximately 50% of the way up the bend
::*Bend shown in red, boundary between subiculum and PHC shown in green
::*Subiculum is superior to boundary
'''Separating Subiculum from CA1 (SubCA1)'''
::*Both anterior and posterior slices
::*''Anterior'': boundary more lateral; draw boundary underneath "bump" where the curve of the hippocampus comes in, bisecting it
:::* Bump shown in red, boundary between Sub and CA1 shown in blue
:::* Sub is medial to the boundary, CA1 is lateral
::: [[File:unfolding-SubCA1_anterior.jpg]]
::*''Posterior'': boundary more medial; draw boundary where the hippocampus pinches off into a tear-drop shape, or folds into itself
:::*Teardrop shown in red, boundary between Sub and CA1 shown in blue
:::*Sub is medial to the boundary, CA1 is lateral
:::[[File:unfolding-SubCA1_posterior.jpg]]
'''Separating CA1 from CA23DG (CA1CA23DG)'''
::[[File:unfolding-CA1CA23DG.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend (on the path where the hippocampal fissure would extend to in the hippocampal head)
::*Bend shown in red; boundary between CA1CA23DG shown in green
'''Separating ERC from Subiculum (ERCSub)'''
::[[File:unfolding-ERCSub.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*If you were to continue the lateral boundary of the hippocampus inwards medially, it would divide the hippocampus and the ERC
::*Draw boundary along this divide, perpendicular to gray matter ribbon
::*Lateral boundary shown in red, boundary between ERC and Sub shown in yellow
'''Separating PRC from ERC (PRCERC)'''
::[[File:unfolding-PRCERC.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the medial side of the collateral sulcus (the side of the collateral sulcus closer to the hippocampal head)
::*Collateral sulcus outlined in yellow, boundary between PRC and ERC in green
::*ERC medial to boundary, PRC lateral
'''Anterior CA fields and Dentate Gyrus (AntCADG)'''
::[[File:unfolding-AntCADG.jpg]]
::*Only one slice: draw on the first slice anterior to the hippocampal head slice (this should be the slice where you first see undulations going in the Posterior to Anterior direction)
::*Draw boundary straight through middle of CADG area, and extend all the way laterally to the CA1CA23DG boundary (go through the middle of the hippocampal head between the fissure and the top of the head)
::*Undulations highlighted in red; CA1CA23DG boundary in green; AntCADG boundary in white
'''Creating A/P boundary (ERCPRCPHC)'''
::[[File:unfolding-ERCPRCPHC.jpg]]
::*Only one slice: draw on the hippocampal head slice
::*Starting at the ERCSub boundary, draw a line in the middle of the gray matter ribbon up and over the collateral sulcus, all the way out to the Fus boundary
::* ERCSub and Fus boundaries shown in yellow
::* ERCPRCPHC boundary shown in white

===Directory Outline: How to Open FSLView Through Terminal===
:Below is an outline for the directory path. In order to open files for segmentation, interpolation, and demarcation in the unfolding process, you must be able to navigate the Terminal.

::[[File:unfolding-directory_route.png]]

The best way to open FSLview in order to do demarcations is through the FSLview path in ''Terminal''. Below are the following steps to open a file for demarcations.

#ssh -X johnsmith@hoffman2.idre.ucla.edu
: This is your login. You must have a '''hoffman''' account to access ''Terminal''
#/u/home/FMRI/sbook/data/AD/subjects
: This is your homebase directory. Once logged into hoffman, you will be able to access the path of directories seen above.
::For each subject, there is a '''nii''' directory and a '''analysis''' directory, which contain information used for demarcations.
:::The '''nii''' directory contains the image files for the brain scans.
:::The '''analysis''' directory contains the subdirectories '''preprocessing''' and '''structural'''.
::::The preprocessing directory may also contain the hhr structural image file, as seen in the nii directory .
::::The structural directory contains the '''unfold''' directory which contains folders for ''segmentation'', ''interpolation'', and ''demarcations''.
#cd AD_10210/2008XXXX/analysis/structural/unfold
:In this unfold directory, you can check if the hhr image file is already in preprocessing. If the hhr image file is already in the preprocessing directory, it can be opened directly in FSL view.
#fslview hhr_struct_6.nii.gz
: If the hhr image is not in the preprocessing directory, you can copy the image from the '''nii''' directory into the '''preprocessing''' and then open it in FSL view.
#cd ../../../subjects/AD_1XXXXX
#cd nii
#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz
##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)

==External Links==
*[https://www.virtualbox.org/ Virtual Box: Virtual machine software]
*[http://white.stanford.edu/~brian/mri/segmentUnfold.htm MrGray Segmentation software for Windows]
*[http://www.cygwin.com/ Cygwin Command-line interface for Windows]
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Home Page]

Unfolding

2014-01-28T01:44:03Z

Ccn admin: /* Segmentation */

There are several steps to successfully unfolding the high resolution scans of the hippocampus. The details for this section fall into the broad categories of segmentation, interpolation, demarcations, and calculating thickness. A knowledge of command line is necessary, as well as obtaining the tools for each step.

==Tools Required==
*A copy of Windows
*A virtual machine emulator
*A command line interface to connect to [[Hoffman2|hoffman]]
*MrGray (Windows only)
*Matlab

==Segmentation==
===Overview===
The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

===Getting Started: The Initial Segmentation Checklist===
#Export all of your vAnatomyCrop.dat files to a PC (ftp using binary).
#Run the program mrGray
#Create a new project and name it after your subject. Use the following nomenclature:
::AD_#####
:::ex. AD_12345

For a subject with the Small ID 12345, who was scanned on May 25th, 2012, the following would be the subject entry in /u/home/data/sbook/data/AD/subjects:
::subj ID: AD_12345
::date: 20120525 (yyyymmdd)
::And it would be in the following path:
:::/u/home/sbook/data/AD/subjects/AD_12345/20120525/... etc etc.

Subjects file names should look like:
::subject ID: AD_12345
::subject scan date: 20120525
::segmentation: AD_12345_seg
::interpolation: AD_12345_interpright or AD_12345_interpleft

Once you have completed the segmentation session make sure to update our filemaker tab in objective fitness spreadsheet
::Select name for new project in AD/subjects/AD_XXXXX/SCANDATE/analysis/structural/unfold/segmentation
:::Select vAnatomyCrop.dat
:::Figure out which slices to segment based on anatomical guidelines.
::::*Anteriorly, choosing the last slice in which hippocampal head is visible is a consistent start point we've used

::Below are anatomical diagrams of the hippocampus and what to look for:
[[File:unfolding-Anat.png]]
:::Figure 1. Anatomical diagram, with an inferior view of the whole brain at the left, an inferior view of the temporal lobe at the center, and coronal sections from the two indicated slices at the right. A: Anterior slice through entorhinal cortex. B: Posterior slice through parahippocampal cortex. ERC, entorhinal cortex; PRC, perirhinal cortex; PHC, parahippocampal cortex; FG, fusiform gyrus; Sub, subiculum; CA 1,cornu ammonis 1; CA 2,3, CA fields 2 and 3; DG, dentate gyrus; CoS, collateral sulcus.
[[File:unfolding-Hipp.png]]
:::Figure 2. Coronal view of right side of the hippocampus. In the coronal plane the hippocampus and parahippocampal gyrus form an S-shaped configuration. The hippocampus itself consists of two interlocking C-shaped structures: the cornu ammonis and the dentate gyrus. Histologically, the hippocampus is further divided into 4 sections CA1 to CA4.

Once file is created, you may begin segmentation process:
#Segment the white matter 1st (colored in beige) (red in our lab), using a pixel size of 3 pixels minimum
#Select white matter with the checkbox at the right
#Another checkbox indicates the highlight size (use 3)
#The left mouse button highlights a pixel, and the right mouse button deselects pixels
#Then, segment the CSF (colored in yellow) (blue in our lab), imposing a thin boundary on the segmentation. (You want it thin because you will expand it after the interpolation step).
#Save the segmentation (File -> Classification -> Save as with the above nomenclature).
::*'''Save early, save often.'''

Here is an example of an initial segmentation: Starting anteriorly and ending posteriorly:

:[[File:unfolding-Seg_P1.png]]
:[[File:unfolding-Seg_P2.png]]

==Interpolation==
Explain [[interpolation]] here.

To load an existing project, when you're in MrGray, you'll click on Load project and you can select any .mrp file.
These will be named AD_1XXXX_interpleft or _interpright. It will then appear and you should be able to see the CSF
and white matter masks if they are selected in the toolbar.

Create a new interpolation file; these are the steps you will take:

# Open the menu and select File > New Project
# In the first window go to the subject's unfold directory (ie. ...AD/subjects/AD_1XXXX/2012####/analysis/structural/unfold/interpolation)
# Name the project AD_1XXXX_interpleft or AD_1XXXX_interpright and hit enter
# In the second window select the Volume anatomy file for the interpolation file (vAnatInterp.dat file) and hit enter
# When the image displays, you will now go to the File menu again and then to "Classification". Then click "load classification file".
# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.
# Check to make sure the masks align correctly.

==Demarcations==

===Getting Started===
After segmentation and interpolation, [[demarcations]] create the boundaries for the different region of the hippocampus. These boundaries can be conveniently drawn using FSLview. Open your hire structural image. Be sure this is the same brain that you used for the unfolding process. It is important to note that these images are in radiological convention, so if you're drawing on the right side of the screen, this is actually the left hemisphere. Look at your notes to determine which slices were segmented and used for unfolding; only draw boundaries on the slices that have been segmented. To create a new boundary, go to the file menu and select "Create Mask." In the lower left corner, you'll see a blue "i"; click on this to re-name your boundary as needed, and to select the color you'd like to draw with. To zoom in on the MTL, first go to View/Single, and then expland the coronal image. Use the zoom tool to magnify the MTL. Click on the pencil tool, and make adjustments as desired. A brightness with typically a max of 1 and a small pencil size work best. If using a mouse, the left button draws the boundary and the ctrl+ left button erases. When saving, be sure to save to your Demarcations directory, and to use the proper naming convention. It is best to complete one boundary at a time across all slices, and then move on to the next boundary.

===General Tips===
Before starting to draw, you want to first identify the slice where the hippocampal head begins. It is important to note that where the hippocampal head "begins" means where it begins when going in the Posterior to Anterior direction. This slice, which will be called the '''hippocampal head slice''' throughout the rest of these instructions is where the anterior structures will start. Also, drawing shorter/smaller boundaries will reduce variability once projected onto the flat maps, giving you a straighter line. In general, boundary doesn't need to cross the entire gray matter area; keep the boundary towards the medial or superior side of things, as appropriate.

===Naming Convention===
Boundaries drawn on all the slices:
*'''Fus'''(Fusiform)
* '''CollSul'''(Collateral Sulcus)
*'''SubCA1'''(Subiculum-CA1)
* '''CA1CA23DG'''(CA1-CA23DG)
Boundaries drawn on anterior slices only:
*'''ERCSub''' (Entorhinal Coral- Subiculum)
*'''PRCERC''' (Perirhinal Cortex- Entorhinal Cortex)
*'''AntCADG''' (Anterior portion of CA fields and Dentate Gyrus)
* '''ERCPRCPHC''' (Boundary between anterior structures Entorhinal/Perirhinal Cortices and the posterior structure Parahippocampal Cortex)
Boundaries drawn on the posterior slices only:
*'''PHCSub''' (Parahippocampal Cortex- Subiculum)

===Individual Boundaries===
On each of the slices that were segmented, we must determine which boundaries to mark.

'''Fusiform (Fus)'''
::[[File:unfolding-Fus.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the lateral side of the collateral sulcus (on the side closer to the second sulcus)
::*Outline of collateral sulcul shown in red; boundary between sulcus and fusiform gyrus shown in yellow
::*Fusiform is lateral to the boundary
'''Collateral Sulcus (CollSul)'''
::[[File:unfolding-CollSul.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend in the superior tip of the collateral sulcus
::*Outline of collateral sulcus shown in yellow; boundary shown in red
'''Separating PHC from Subiculum (PHCSub)'''
::[[File:unfolding-PHCSub.jpg]]
::*Posterior slices only
::*Begin drawing on the first slice posterior to the hippocampal head slice, and continue to draw on the remainder of the posterior slices
::*Draw boundary perpendicular to the gray matter ribbon approximately 50% of the way up the bend
::*Bend shown in red, boundary between subiculum and PHC shown in green
::*Subiculum is superior to boundary
'''Separating Subiculum from CA1 (SubCA1)'''
::*Both anterior and posterior slices
::*''Anterior'': boundary more lateral; draw boundary underneath "bump" where the curve of the hippocampus comes in, bisecting it
:::* Bump shown in red, boundary between Sub and CA1 shown in blue
:::* Sub is medial to the boundary, CA1 is lateral
::: [[File:unfolding-SubCA1_anterior.jpg]]
::*''Posterior'': boundary more medial; draw boundary where the hippocampus pinches off into a tear-drop shape, or folds into itself
:::*Teardrop shown in red, boundary between Sub and CA1 shown in blue
:::*Sub is medial to the boundary, CA1 is lateral
:::[[File:unfolding-SubCA1_posterior.jpg]]
'''Separating CA1 from CA23DG (CA1CA23DG)'''
::[[File:unfolding-CA1CA23DG.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend (on the path where the hippocampal fissure would extend to in the hippocampal head)
::*Bend shown in red; boundary between CA1CA23DG shown in green
'''Separating ERC from Subiculum (ERCSub)'''
::[[File:unfolding-ERCSub.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*If you were to continue the lateral boundary of the hippocampus inwards medially, it would divide the hippocampus and the ERC
::*Draw boundary along this divide, perpendicular to gray matter ribbon
::*Lateral boundary shown in red, boundary between ERC and Sub shown in yellow
'''Separating PRC from ERC (PRCERC)'''
::[[File:unfolding-PRCERC.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the medial side of the collateral sulcus (the side of the collateral sulcus closer to the hippocampal head)
::*Collateral sulcus outlined in yellow, boundary between PRC and ERC in green
::*ERC medial to boundary, PRC lateral
'''Anterior CA fields and Dentate Gyrus (AntCADG)'''
::[[File:unfolding-AntCADG.jpg]]
::*Only one slice: draw on the first slice anterior to the hippocampal head slice (this should be the slice where you first see undulations going in the Posterior to Anterior direction)
::*Draw boundary straight through middle of CADG area, and extend all the way laterally to the CA1CA23DG boundary (go through the middle of the hippocampal head between the fissure and the top of the head)
::*Undulations highlighted in red; CA1CA23DG boundary in green; AntCADG boundary in white
'''Creating A/P boundary (ERCPRCPHC)'''
::[[File:unfolding-ERCPRCPHC.jpg]]
::*Only one slice: draw on the hippocampal head slice
::*Starting at the ERCSub boundary, draw a line in the middle of the gray matter ribbon up and over the collateral sulcus, all the way out to the Fus boundary
::* ERCSub and Fus boundaries shown in yellow
::* ERCPRCPHC boundary shown in white

===Directory Outline: How to Open FSLView Through Terminal===
:Below is an outline for the directory path. In order to open files for segmentation, interpolation, and demarcation in the unfolding process, you must be able to navigate the Terminal.

::[[File:unfolding-directory_route.png]]

The best way to open FSLview in order to do demarcations is through the FSLview path in ''Terminal''. Below are the following steps to open a file for demarcations.

#ssh -X johnsmith@hoffman2.idre.ucla.edu
: This is your login. You must have a '''hoffman''' account to access ''Terminal''
#/u/home/FMRI/sbook/data/AD/subjects
: This is your homebase directory. Once logged into hoffman, you will be able to access the path of directories seen above.
::For each subject, there is a '''nii''' directory and a '''analysis''' directory, which contain information used for demarcations.
:::The '''nii''' directory contains the image files for the brain scans.
:::The '''analysis''' directory contains the subdirectories '''preprocessing''' and '''structural'''.
::::The preprocessing directory may also contain the hhr structural image file, as seen in the nii directory .
::::The structural directory contains the '''unfold''' directory which contains folders for ''segmentation'', ''interpolation'', and ''demarcations''.
#cd AD_10210/2008XXXX/analysis/structural/unfold
:In this unfold directory, you can check if the hhr image file is already in preprocessing. If the hhr image file is already in the preprocessing directory, it can be opened directly in FSL view.
#fslview hhr_struct_6.nii.gz
: If the hhr image is not in the preprocessing directory, you can copy the image from the '''nii''' directory into the '''preprocessing''' and then open it in FSL view.
#cd ../../../subjects/AD_1XXXXX
#cd nii
#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz
##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)

==External Links==
*[https://www.virtualbox.org/ Virtual Box: Virtual machine software]
*[http://white.stanford.edu/~brian/mri/segmentUnfold.htm MrGray Segmentation software for Windows]
*[http://www.cygwin.com/ Cygwin Command-line interface for Windows]
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Home Page]

File:Unfolding-Seg P1.png

2014-01-28T01:43:38Z

Ccn admin:

File:Unfolding-Seg P2.png

2014-01-28T01:43:12Z

Ccn admin:

File:Unfolding-Hipp.png

2014-01-28T01:40:21Z

Ccn admin:

Unfolding

2014-01-28T01:38:22Z

Ccn admin:

There are several steps to successfully unfolding the high resolution scans of the hippocampus. The details for this section fall into the broad categories of segmentation, interpolation, demarcations, and calculating thickness. A knowledge of command line is necessary, as well as obtaining the tools for each step.

==Tools Required==
*A copy of Windows
*A virtual machine emulator
*A command line interface to connect to [[Hoffman2|hoffman]]
*MrGray (Windows only)
*Matlab

==Segmentation==
===Overview===
The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

===Getting Started: The Initial Segmentation Checklist===
#Export all of your vAnatomyCrop.dat files to a PC (ftp using binary).
#Run the program mrGray
#Create a new project and name it after your subject. Use the following nomenclature:
::AD_#####
:::ex. AD_12345

For a subject with the Small ID 12345, who was scanned on May 25th, 2012, the following would be the subject entry in /u/home/data/sbook/data/AD/subjects:
::subj ID: AD_12345
::date: 20120525 (yyyymmdd)
::And it would be in the following path:
:::/u/home/sbook/data/AD/subjects/AD_12345/20120525/... etc etc.

Subjects file names should look like:
::subject ID: AD_12345
::subject scan date: 20120525
::segmentation: AD_12345_seg
::interpolation: AD_12345_interpright or AD_12345_interpleft

Once you have completed the segmentation session make sure to update our filemaker tab in objective fitness spreadsheet
::Select name for new project in AD/subjects/AD_XXXXX/SCANDATE/analysis/structural/unfold/segmentation
:::Select vAnatomyCrop.dat
:::Figure out which slices to segment based on anatomical guidelines.
::::*Anteriorly, choosing the last slice in which hippocampal head is visible is a consistent start point we've used

::Below are anatomical diagrams of the hippocampus and what to look for:
[[File:unfolding-Anat.png]]
:::Figure 1. Anatomical diagram, with an inferior view of the whole brain at the left, an inferior view of the temporal lobe at the center, and coronal sections from the two indicated slices at the right. A: Anterior slice through entorhinal cortex. B: Posterior slice through parahippocampal cortex. ERC, entorhinal cortex; PRC, perirhinal cortex; PHC, parahippocampal cortex; FG, fusiform gyrus; Sub, subiculum; CA 1,cornu ammonis 1; CA 2,3, CA fields 2 and 3; DG, dentate gyrus; CoS, collateral sulcus.
[[File:unfolding-hipp.png]]
:::Figure 2. Coronal view of right side of the hippocampus. In the coronal plane the hippocampus and parahippocampal gyrus form an S-shaped configuration. The hippocampus itself consists of two interlocking C-shaped structures: the cornu ammonis and the dentate gyrus. Histologically, the hippocampus is further divided into 4 sections CA1 to CA4.

Once file is created, you may begin segmentation process:
#Segment the white matter 1st (colored in beige) (red in our lab), using a pixel size of 3 pixels minimum
#Select white matter with the checkbox at the right
#Another checkbox indicates the highlight size (use 3)
#The left mouse button highlights a pixel, and the right mouse button deselects pixels
#Then, segment the CSF (colored in yellow) (blue in our lab), imposing a thin boundary on the segmentation. (You want it thin because you will expand it after the interpolation step).
#Save the segmentation (File -> Classification -> Save as with the above nomenclature).
::*'''Save early, save often.'''

Here is an example of an initial segmentation: Starting anteriorly and ending posteriorly:

:[[File:unfolding-seg_part_1.png]]
:[[File:unfolding-seg_part_2.png]]

==Interpolation==
Explain [[interpolation]] here.

To load an existing project, when you're in MrGray, you'll click on Load project and you can select any .mrp file.
These will be named AD_1XXXX_interpleft or _interpright. It will then appear and you should be able to see the CSF
and white matter masks if they are selected in the toolbar.

Create a new interpolation file; these are the steps you will take:

# Open the menu and select File > New Project
# In the first window go to the subject's unfold directory (ie. ...AD/subjects/AD_1XXXX/2012####/analysis/structural/unfold/interpolation)
# Name the project AD_1XXXX_interpleft or AD_1XXXX_interpright and hit enter
# In the second window select the Volume anatomy file for the interpolation file (vAnatInterp.dat file) and hit enter
# When the image displays, you will now go to the File menu again and then to "Classification". Then click "load classification file".
# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.
# Check to make sure the masks align correctly.

==Demarcations==

===Getting Started===
After segmentation and interpolation, [[demarcations]] create the boundaries for the different region of the hippocampus. These boundaries can be conveniently drawn using FSLview. Open your hire structural image. Be sure this is the same brain that you used for the unfolding process. It is important to note that these images are in radiological convention, so if you're drawing on the right side of the screen, this is actually the left hemisphere. Look at your notes to determine which slices were segmented and used for unfolding; only draw boundaries on the slices that have been segmented. To create a new boundary, go to the file menu and select "Create Mask." In the lower left corner, you'll see a blue "i"; click on this to re-name your boundary as needed, and to select the color you'd like to draw with. To zoom in on the MTL, first go to View/Single, and then expland the coronal image. Use the zoom tool to magnify the MTL. Click on the pencil tool, and make adjustments as desired. A brightness with typically a max of 1 and a small pencil size work best. If using a mouse, the left button draws the boundary and the ctrl+ left button erases. When saving, be sure to save to your Demarcations directory, and to use the proper naming convention. It is best to complete one boundary at a time across all slices, and then move on to the next boundary.

===General Tips===
Before starting to draw, you want to first identify the slice where the hippocampal head begins. It is important to note that where the hippocampal head "begins" means where it begins when going in the Posterior to Anterior direction. This slice, which will be called the '''hippocampal head slice''' throughout the rest of these instructions is where the anterior structures will start. Also, drawing shorter/smaller boundaries will reduce variability once projected onto the flat maps, giving you a straighter line. In general, boundary doesn't need to cross the entire gray matter area; keep the boundary towards the medial or superior side of things, as appropriate.

===Naming Convention===
Boundaries drawn on all the slices:
*'''Fus'''(Fusiform)
* '''CollSul'''(Collateral Sulcus)
*'''SubCA1'''(Subiculum-CA1)
* '''CA1CA23DG'''(CA1-CA23DG)
Boundaries drawn on anterior slices only:
*'''ERCSub''' (Entorhinal Coral- Subiculum)
*'''PRCERC''' (Perirhinal Cortex- Entorhinal Cortex)
*'''AntCADG''' (Anterior portion of CA fields and Dentate Gyrus)
* '''ERCPRCPHC''' (Boundary between anterior structures Entorhinal/Perirhinal Cortices and the posterior structure Parahippocampal Cortex)
Boundaries drawn on the posterior slices only:
*'''PHCSub''' (Parahippocampal Cortex- Subiculum)

===Individual Boundaries===
On each of the slices that were segmented, we must determine which boundaries to mark.

'''Fusiform (Fus)'''
::[[File:unfolding-Fus.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the lateral side of the collateral sulcus (on the side closer to the second sulcus)
::*Outline of collateral sulcul shown in red; boundary between sulcus and fusiform gyrus shown in yellow
::*Fusiform is lateral to the boundary
'''Collateral Sulcus (CollSul)'''
::[[File:unfolding-CollSul.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend in the superior tip of the collateral sulcus
::*Outline of collateral sulcus shown in yellow; boundary shown in red
'''Separating PHC from Subiculum (PHCSub)'''
::[[File:unfolding-PHCSub.jpg]]
::*Posterior slices only
::*Begin drawing on the first slice posterior to the hippocampal head slice, and continue to draw on the remainder of the posterior slices
::*Draw boundary perpendicular to the gray matter ribbon approximately 50% of the way up the bend
::*Bend shown in red, boundary between subiculum and PHC shown in green
::*Subiculum is superior to boundary
'''Separating Subiculum from CA1 (SubCA1)'''
::*Both anterior and posterior slices
::*''Anterior'': boundary more lateral; draw boundary underneath "bump" where the curve of the hippocampus comes in, bisecting it
:::* Bump shown in red, boundary between Sub and CA1 shown in blue
:::* Sub is medial to the boundary, CA1 is lateral
::: [[File:unfolding-SubCA1_anterior.jpg]]
::*''Posterior'': boundary more medial; draw boundary where the hippocampus pinches off into a tear-drop shape, or folds into itself
:::*Teardrop shown in red, boundary between Sub and CA1 shown in blue
:::*Sub is medial to the boundary, CA1 is lateral
:::[[File:unfolding-SubCA1_posterior.jpg]]
'''Separating CA1 from CA23DG (CA1CA23DG)'''
::[[File:unfolding-CA1CA23DG.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend (on the path where the hippocampal fissure would extend to in the hippocampal head)
::*Bend shown in red; boundary between CA1CA23DG shown in green
'''Separating ERC from Subiculum (ERCSub)'''
::[[File:unfolding-ERCSub.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*If you were to continue the lateral boundary of the hippocampus inwards medially, it would divide the hippocampus and the ERC
::*Draw boundary along this divide, perpendicular to gray matter ribbon
::*Lateral boundary shown in red, boundary between ERC and Sub shown in yellow
'''Separating PRC from ERC (PRCERC)'''
::[[File:unfolding-PRCERC.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the medial side of the collateral sulcus (the side of the collateral sulcus closer to the hippocampal head)
::*Collateral sulcus outlined in yellow, boundary between PRC and ERC in green
::*ERC medial to boundary, PRC lateral
'''Anterior CA fields and Dentate Gyrus (AntCADG)'''
::[[File:unfolding-AntCADG.jpg]]
::*Only one slice: draw on the first slice anterior to the hippocampal head slice (this should be the slice where you first see undulations going in the Posterior to Anterior direction)
::*Draw boundary straight through middle of CADG area, and extend all the way laterally to the CA1CA23DG boundary (go through the middle of the hippocampal head between the fissure and the top of the head)
::*Undulations highlighted in red; CA1CA23DG boundary in green; AntCADG boundary in white
'''Creating A/P boundary (ERCPRCPHC)'''
::[[File:unfolding-ERCPRCPHC.jpg]]
::*Only one slice: draw on the hippocampal head slice
::*Starting at the ERCSub boundary, draw a line in the middle of the gray matter ribbon up and over the collateral sulcus, all the way out to the Fus boundary
::* ERCSub and Fus boundaries shown in yellow
::* ERCPRCPHC boundary shown in white

===Directory Outline: How to Open FSLView Through Terminal===
:Below is an outline for the directory path. In order to open files for segmentation, interpolation, and demarcation in the unfolding process, you must be able to navigate the Terminal.

::[[File:unfolding-directory_route.png]]

The best way to open FSLview in order to do demarcations is through the FSLview path in ''Terminal''. Below are the following steps to open a file for demarcations.

#ssh -X johnsmith@hoffman2.idre.ucla.edu
: This is your login. You must have a '''hoffman''' account to access ''Terminal''
#/u/home/FMRI/sbook/data/AD/subjects
: This is your homebase directory. Once logged into hoffman, you will be able to access the path of directories seen above.
::For each subject, there is a '''nii''' directory and a '''analysis''' directory, which contain information used for demarcations.
:::The '''nii''' directory contains the image files for the brain scans.
:::The '''analysis''' directory contains the subdirectories '''preprocessing''' and '''structural'''.
::::The preprocessing directory may also contain the hhr structural image file, as seen in the nii directory .
::::The structural directory contains the '''unfold''' directory which contains folders for ''segmentation'', ''interpolation'', and ''demarcations''.
#cd AD_10210/2008XXXX/analysis/structural/unfold
:In this unfold directory, you can check if the hhr image file is already in preprocessing. If the hhr image file is already in the preprocessing directory, it can be opened directly in FSL view.
#fslview hhr_struct_6.nii.gz
: If the hhr image is not in the preprocessing directory, you can copy the image from the '''nii''' directory into the '''preprocessing''' and then open it in FSL view.
#cd ../../../subjects/AD_1XXXXX
#cd nii
#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz
##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)

==External Links==
*[https://www.virtualbox.org/ Virtual Box: Virtual machine software]
*[http://white.stanford.edu/~brian/mri/segmentUnfold.htm MrGray Segmentation software for Windows]
*[http://www.cygwin.com/ Cygwin Command-line interface for Windows]
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Home Page]

File:Unfolding-Anat.png

2014-01-28T01:37:43Z

Ccn admin:

Unfolding

2014-01-28T01:28:56Z

Ccn admin:

There are several steps to successfully unfolding the high resolution scans of the hippocampus. The details for this section fall into the broad categories of segmentation, interpolation, demarcations, and calculating thickness. A knowledge of command line is necessary, as well as obtaining the tools for each step.

==Tools Required==
*A copy of Windows
*A virtual machine emulator
*A command line interface to connect to [[Hoffman2|hoffman]]
*MrGray (Windows only)
*Matlab

==Segmentation==
===Overview===
The goal of [[segmentation]] is to create a strip of gray matter in the hippocampus by locating the boundaries of the hippocampus in the brain. Using FMRI technology, the brain is sliced anteriorly to posteriorly to obtain slices of all parts of the hippocampus, creating a 2D version of the 3D hippocampus that can be mapped and analyzed. After opening [[VirtualBox]], we run a computer program, [[MrGray Segmentation software for Windows]], where we can view and find all the slices of the brain that show a portion of the hippocampus. On these slices,the hippocampal gray matter is surrounded by white matter and cerebral spinal fluid (CSF). We must mark the surrounding white matter and CSF respectively to obtain our strip of gray matter in between. The CSF material is the strip of atrophy on the interior of the gray matter, which begins at the hippocampal fissure, follows down to the collateral sulcus, and finishes after the second sulcus. The white matter is the material on the exterior portion of the gray matter. It is important to note that the shape of the hippocampal head changes from anterior to posterior in the brain. On the anterior slices, the hippocampal head has a long, oval shape. In the posterior slices, the hippocampal head has a round, almond shape. On the anterior slices, the CSF matter comes up to meet the white matter at the hippocampus head and also continues through the second sulcus through the gray matter to close off our strip. In the posterior slices, the CSF still continues through the second sulcus to the gray matter to close off the strip, but the white matter comes down to the CSF at the hippocampal fissure on the hippocampal head.

===Getting Started: The Initial Segmentation Checklist===
#Export all of your vAnatomyCrop.dat files to a PC (ftp using binary).
#Run the program mrGray
#Create a new project and name it after your subject. Use the following nomenclature:
::AD_#####
:::ex. AD_12345

For a subject with the Small ID 12345, who was scanned on May 25th, 2012, the following would be the subject entry in /u/home/data/sbook/data/AD/subjects:
::subj ID: AD_12345
::date: 20120525 (yyyymmdd)
::And it would be in the following path:
:::/u/home/sbook/data/AD/subjects/AD_12345/20120525/... etc etc.

Subjects file names should look like:
::subject ID: AD_12345
::subject scan date: 20120525
::segmentation: AD_12345_seg
::interpolation: AD_12345_interpright or AD_12345_interpleft

Once you have completed the segmentation session make sure to update our filemaker tab in objective fitness spreadsheet
::Select name for new project in AD/subjects/AD_XXXXX/SCANDATE/analysis/structural/unfold/segmentation
:::Select vAnatomyCrop.dat
:::Figure out which slices to segment based on anatomical guidelines.
::::*Anteriorly, choosing the last slice in which hippocampal head is visible is a consistent start point we've used

::Below are anatomical diagrams of the hippocampus and what to look for:
[[File:unfolding-anat.png]]
:::Figure 1. Anatomical diagram, with an inferior view of the whole brain at the left, an inferior view of the temporal lobe at the center, and coronal sections from the two indicated slices at the right. A: Anterior slice through entorhinal cortex. B: Posterior slice through parahippocampal cortex. ERC, entorhinal cortex; PRC, perirhinal cortex; PHC, parahippocampal cortex; FG, fusiform gyrus; Sub, subiculum; CA 1,cornu ammonis 1; CA 2,3, CA fields 2 and 3; DG, dentate gyrus; CoS, collateral sulcus.
[[File:unfolding-hipp.png]]
:::Figure 2. Coronal view of right side of the hippocampus. In the coronal plane the hippocampus and parahippocampal gyrus form an S-shaped configuration. The hippocampus itself consists of two interlocking C-shaped structures: the cornu ammonis and the dentate gyrus. Histologically, the hippocampus is further divided into 4 sections CA1 to CA4.

Once file is created, you may begin segmentation process:
#Segment the white matter 1st (colored in beige) (red in our lab), using a pixel size of 3 pixels minimum
#Select white matter with the checkbox at the right
#Another checkbox indicates the highlight size (use 3)
#The left mouse button highlights a pixel, and the right mouse button deselects pixels
#Then, segment the CSF (colored in yellow) (blue in our lab), imposing a thin boundary on the segmentation. (You want it thin because you will expand it after the interpolation step).
#Save the segmentation (File -> Classification -> Save as with the above nomenclature).
::*'''Save early, save often.'''

Here is an example of an initial segmentation: Starting anteriorly and ending posteriorly:

:[[File:unfolding-seg_part_1.png]]
:[[File:unfolding-seg_part_2.png]]

==Interpolation==
Explain [[interpolation]] here.

To load an existing project, when you're in MrGray, you'll click on Load project and you can select any .mrp file.
These will be named AD_1XXXX_interpleft or _interpright. It will then appear and you should be able to see the CSF
and white matter masks if they are selected in the toolbar.

Create a new interpolation file; these are the steps you will take:

# Open the menu and select File > New Project
# In the first window go to the subject's unfold directory (ie. ...AD/subjects/AD_1XXXX/2012####/analysis/structural/unfold/interpolation)
# Name the project AD_1XXXX_interpleft or AD_1XXXX_interpright and hit enter
# In the second window select the Volume anatomy file for the interpolation file (vAnatInterp.dat file) and hit enter
# When the image displays, you will now go to the File menu again and then to "Classification". Then click "load classification file".
# The window that pops up will ask you to select a class file. This will be AD_1XXXX_interpright or interpleft that already exists in the directory. Select the side for which you created and hit enter.
# Check to make sure the masks align correctly.

==Demarcations==

===Getting Started===
After segmentation and interpolation, [[demarcations]] create the boundaries for the different region of the hippocampus. These boundaries can be conveniently drawn using FSLview. Open your hire structural image. Be sure this is the same brain that you used for the unfolding process. It is important to note that these images are in radiological convention, so if you're drawing on the right side of the screen, this is actually the left hemisphere. Look at your notes to determine which slices were segmented and used for unfolding; only draw boundaries on the slices that have been segmented. To create a new boundary, go to the file menu and select "Create Mask." In the lower left corner, you'll see a blue "i"; click on this to re-name your boundary as needed, and to select the color you'd like to draw with. To zoom in on the MTL, first go to View/Single, and then expland the coronal image. Use the zoom tool to magnify the MTL. Click on the pencil tool, and make adjustments as desired. A brightness with typically a max of 1 and a small pencil size work best. If using a mouse, the left button draws the boundary and the ctrl+ left button erases. When saving, be sure to save to your Demarcations directory, and to use the proper naming convention. It is best to complete one boundary at a time across all slices, and then move on to the next boundary.

===General Tips===
Before starting to draw, you want to first identify the slice where the hippocampal head begins. It is important to note that where the hippocampal head "begins" means where it begins when going in the Posterior to Anterior direction. This slice, which will be called the '''hippocampal head slice''' throughout the rest of these instructions is where the anterior structures will start. Also, drawing shorter/smaller boundaries will reduce variability once projected onto the flat maps, giving you a straighter line. In general, boundary doesn't need to cross the entire gray matter area; keep the boundary towards the medial or superior side of things, as appropriate.

===Naming Convention===
Boundaries drawn on all the slices:
*'''Fus'''(Fusiform)
* '''CollSul'''(Collateral Sulcus)
*'''SubCA1'''(Subiculum-CA1)
* '''CA1CA23DG'''(CA1-CA23DG)
Boundaries drawn on anterior slices only:
*'''ERCSub''' (Entorhinal Coral- Subiculum)
*'''PRCERC''' (Perirhinal Cortex- Entorhinal Cortex)
*'''AntCADG''' (Anterior portion of CA fields and Dentate Gyrus)
* '''ERCPRCPHC''' (Boundary between anterior structures Entorhinal/Perirhinal Cortices and the posterior structure Parahippocampal Cortex)
Boundaries drawn on the posterior slices only:
*'''PHCSub''' (Parahippocampal Cortex- Subiculum)

===Individual Boundaries===
On each of the slices that were segmented, we must determine which boundaries to mark.

'''Fusiform (Fus)'''
::[[File:unfolding-Fus.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the lateral side of the collateral sulcus (on the side closer to the second sulcus)
::*Outline of collateral sulcul shown in red; boundary between sulcus and fusiform gyrus shown in yellow
::*Fusiform is lateral to the boundary
'''Collateral Sulcus (CollSul)'''
::[[File:unfolding-CollSul.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend in the superior tip of the collateral sulcus
::*Outline of collateral sulcus shown in yellow; boundary shown in red
'''Separating PHC from Subiculum (PHCSub)'''
::[[File:unfolding-PHCSub.jpg]]
::*Posterior slices only
::*Begin drawing on the first slice posterior to the hippocampal head slice, and continue to draw on the remainder of the posterior slices
::*Draw boundary perpendicular to the gray matter ribbon approximately 50% of the way up the bend
::*Bend shown in red, boundary between subiculum and PHC shown in green
::*Subiculum is superior to boundary
'''Separating Subiculum from CA1 (SubCA1)'''
::*Both anterior and posterior slices
::*''Anterior'': boundary more lateral; draw boundary underneath "bump" where the curve of the hippocampus comes in, bisecting it
:::* Bump shown in red, boundary between Sub and CA1 shown in blue
:::* Sub is medial to the boundary, CA1 is lateral
::: [[File:unfolding-SubCA1_anterior.jpg]]
::*''Posterior'': boundary more medial; draw boundary where the hippocampus pinches off into a tear-drop shape, or folds into itself
:::*Teardrop shown in red, boundary between Sub and CA1 shown in blue
:::*Sub is medial to the boundary, CA1 is lateral
:::[[File:unfolding-SubCA1_posterior.jpg]]
'''Separating CA1 from CA23DG (CA1CA23DG)'''
::[[File:unfolding-CA1CA23DG.jpg]]
::*Both anterior and posterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the bend (on the path where the hippocampal fissure would extend to in the hippocampal head)
::*Bend shown in red; boundary between CA1CA23DG shown in green
'''Separating ERC from Subiculum (ERCSub)'''
::[[File:unfolding-ERCSub.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*If you were to continue the lateral boundary of the hippocampus inwards medially, it would divide the hippocampus and the ERC
::*Draw boundary along this divide, perpendicular to gray matter ribbon
::*Lateral boundary shown in red, boundary between ERC and Sub shown in yellow
'''Separating PRC from ERC (PRCERC)'''
::[[File:unfolding-PRCERC.jpg]]
::*Anterior slices only
::*Begin drawing on hippocampal head slice, and continue to draw on the remainder of the anterior slices
::*Draw boundary perpendicular to the gray matter ribbon at the "elbow" of the medial side of the collateral sulcus (the side of the collateral sulcus closer to the hippocampal head)
::*Collateral sulcus outlined in yellow, boundary between PRC and ERC in green
::*ERC medial to boundary, PRC lateral
'''Anterior CA fields and Dentate Gyrus (AntCADG)'''
::[[File:unfolding-AntCADG.jpg]]
::*Only one slice: draw on the first slice anterior to the hippocampal head slice (this should be the slice where you first see undulations going in the Posterior to Anterior direction)
::*Draw boundary straight through middle of CADG area, and extend all the way laterally to the CA1CA23DG boundary (go through the middle of the hippocampal head between the fissure and the top of the head)
::*Undulations highlighted in red; CA1CA23DG boundary in green; AntCADG boundary in white
'''Creating A/P boundary (ERCPRCPHC)'''
::[[File:unfolding-ERCPRCPHC.jpg]]
::*Only one slice: draw on the hippocampal head slice
::*Starting at the ERCSub boundary, draw a line in the middle of the gray matter ribbon up and over the collateral sulcus, all the way out to the Fus boundary
::* ERCSub and Fus boundaries shown in yellow
::* ERCPRCPHC boundary shown in white

===Directory Outline: How to Open FSLView Through Terminal===
:Below is an outline for the directory path. In order to open files for segmentation, interpolation, and demarcation in the unfolding process, you must be able to navigate the Terminal.

::[[File:unfolding-directory_route.png]]

The best way to open FSLview in order to do demarcations is through the FSLview path in ''Terminal''. Below are the following steps to open a file for demarcations.

#ssh -X johnsmith@hoffman2.idre.ucla.edu
: This is your login. You must have a '''hoffman''' account to access ''Terminal''
#/u/home/FMRI/sbook/data/AD/subjects
: This is your homebase directory. Once logged into hoffman, you will be able to access the path of directories seen above.
::For each subject, there is a '''nii''' directory and a '''analysis''' directory, which contain information used for demarcations.
:::The '''nii''' directory contains the image files for the brain scans.
:::The '''analysis''' directory contains the subdirectories '''preprocessing''' and '''structural'''.
::::The preprocessing directory may also contain the hhr structural image file, as seen in the nii directory .
::::The structural directory contains the '''unfold''' directory which contains folders for ''segmentation'', ''interpolation'', and ''demarcations''.
#cd AD_10210/2008XXXX/analysis/structural/unfold
:In this unfold directory, you can check if the hhr image file is already in preprocessing. If the hhr image file is already in the preprocessing directory, it can be opened directly in FSL view.
#fslview hhr_struct_6.nii.gz
: If the hhr image is not in the preprocessing directory, you can copy the image from the '''nii''' directory into the '''preprocessing''' and then open it in FSL view.
#cd ../../../subjects/AD_1XXXXX
#cd nii
#cp nii/hhr_struct_6.nii.gz ../analysis/preprocessing/hhr_struct_6.nii.gz
##fslview hhr_struct_6.nii.gz (check if this step is fslview analysis/preprocessing/hhr_struct_6.nii.gz)

==External Links==
*[https://www.virtualbox.org/ Virtual Box: Virtual machine software]
*[http://white.stanford.edu/~brian/mri/segmentUnfold.htm MrGray Segmentation software for Windows]
*[http://www.cygwin.com/ Cygwin Command-line interface for Windows]
*[http://www.ats.ucla.edu/clusters/hoffman2/ Hoffman2 Home Page]

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Revised for 2013 course

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Agatha Lerartowicz's Talk 2013/03/13

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Martin Monti's Talk 4/6/2013

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Jesse Rissman's 2013 LEcture Notes

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TMS Lecture for NITP Feb 2013

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E London Lecture Slides 2013/01/30

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Problem Set 2 2012, Optics, Basic Circuits and A/D

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Slides from Dr Susan Bookheimer's talk 2012/10/17

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Solution to Problem Set 1 for PNI-A 2012

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Problem Set 1 for PNIA 2012