Center for Cognitive Neuroscience - User contributions [en]

Hoffman2:Accessing the Cluster

2014-11-20T19:21:58Z

Alhead: /* Troubleshooting */

[[Hoffman2|Back to all things Hoffman2]]

Here are some of our favorite ways to access the Hoffman2 Cluster login nodes.

==SSH - Command Line==
SSH stands for ''Secure Shell'' and is a method of remotely logging into a computer using an encrypted connection. It is a command line tool and is available on most *nix-based operating systems with ports available for Windows.

===Mac/Linux/Unix===
====Simple SSH====
Use the ssh command from a terminal:
ssh login_id@hoffman2.idre.ucla.edu
where login_id is replaced by your cluster user name.

====GUI-Enabled SSH [Recommended]====
Macs (post - Snow Leopard 10.6.x) no longer come with a X Window System Server pre-installed.

'''Before doing the following steps, please install [http://xquartz.macosforge.org/ XQuartz] and restart your computer.'''

For more information about XQuartz, read [http://support.apple.com/kb/ht5293 here].
# Open up X11/XQuartz or Terminal. Both are under ''Applications > Utilities'' on Macs.
# Type the command
#: <pre>$ ssh -X [USERNAME]@hoffman2.idre.ucla.edu</pre>
#: filling in your Hoffman2 username.
#: The <code>-X</code> is for X11 Forwarding so that any graphics that are rendered on Hoffman2 get forwarded to the screen of your computer.
# Press enter and type in your password when it asks for it. No characters or asterisks will show up while you type.
# Provided your typing was good, you will be greeted by the Hoffman2 login message and have successfully SSH into a login node.

===Windows===
# Go [http://hpc.ucla.edu/hoffman2/access/access.php here] and follow the instructions under ''Windows''. We recommend PuTTY or Cgywin.
# Once you have that setup, the process is the same as if you were on a Mac or Linux/Unix machine
# TODO: [More information Coming]

==NX Client - GUI==
: ''The official description of how to do this is found [http://hpc.ucla.edu/hoffman2/access/nx.php here]''
The NX Client program allows you to set up a Virtual Network Computing (VNC)-like session with Hoffman2. This session will keep running even if your Internet connection drops in and out (much like [[Using Screen|screen]] on the command line).

===Mac OS X 10.7+ / Windows / Linux===
==== What You Need====
# Go to the No Machine website ([https://www.nomachine.com/download No Machine]) and download/install the No Machine for Mac OS X/Windows/Linux.
# Hoffman2 NX Client Public Key
#* To get the NX Client Public Key, follow the steps below or email support@ccn.ucla.edu
#** (OSX/Linux) Open up a Terminal and run the following command (replacing USERNAME with your Hoffman2 username)
#**:<code>$ scp USERNAME@hoffman2.idre.ucla.edu:/etc/nxserver/client.id_dsa.key ~/Documents/</code>
#** (Windows) Use a sftp program and download the file /etc/nxserver/client.id_dsa.key on Hoffman2 (hoffman2.idre.ucla.edu)

====Setup====
# Open up No Machine in Application/Desktop and Click Continue.
# A window titled "New Connection" will appear. Fill out the fields accordingly
#* Protocol -- SSH
#* Host -- "hoffman2.idre.ucla.edu"
#* Port -- 22

#* Select "Use the NoMachine login"
#* Select Alternate Server Key and (...) - and find the file (client.id_dsa.key) you downloaded earlier (in your Documents folder).
#* Don't use a proxy
#* Name -- Something like "Hoffman2"

# Double click on the connection you just created (it should be the only one in the list).
# Enter your Hoffman2 username and password and click "OK" (You may also check the box labeled "Save this setting in the configuration file" to avoid retyping this in the future)
# Select "Create a new session". or "New Virtual Desktop"
# In the next menu, select Create new '''GNOME''' virtual desktop.
# A virtual desktop should appear!

Reconnections in this client are not currently supported for Hoffman2, so please make sure to logout and close your connections properly. [http://hpc.ucla.edu/hoffman2/access/nx.php#logout]

====Troubleshooting====
If your NX Client session freezes and you are unable to close it properly, open ''NX Session Administrator'' and disconnect your session from there. This freezing often occurs when your Internet connection is lost abruptly. Another possible cause for freezing is scrolling on certain Windows touchpads.

For more Information [[http://hpc.ucla.edu/hoffman2/access/nx.php Hoffman2 NX Client]]

If you are unable to open Firefox ("Firefox is already running, but is not responding. To open a new window, you must first close the existing Firefox process, or restart your system."), deleting ~/.mozilla might fix the problem. ''Be warned:'' this will erase your profile, including bookmarks, history, saved passwords, etc! For instructions on backing up and restoring profile information, see [https://support.mozilla.org/en-US/kb/back-and-restore-information-firefox-profiles Mozilla Support]. Make sure to perform these actions within No Machine, and not on your local system.

== Change Passwords ==
Once you've logged on and made sure its works, you can change your password to something more rememberable
To change passwords, logon and type:
passwd
It should ask you for your old password and then new ones.

==External Links==
*[http://hpc.ucla.edu/hoffman2/access/access.php Hoffman2 Access]
*[http://hpc.ucla.edu/hoffman2/access/nx.php Hoffman2 via NX Client]
*[[Hoffman2:Accessing_the_Cluster-Historical_Notes | Historical Notes]]

Hoffman2:Accessing the Cluster

2014-11-20T19:20:52Z

Alhead: /* Troubleshooting */ Added information about firefox failing to open

[[Hoffman2|Back to all things Hoffman2]]

Here are some of our favorite ways to access the Hoffman2 Cluster login nodes.

==SSH - Command Line==
SSH stands for ''Secure Shell'' and is a method of remotely logging into a computer using an encrypted connection. It is a command line tool and is available on most *nix-based operating systems with ports available for Windows.

===Mac/Linux/Unix===
====Simple SSH====
Use the ssh command from a terminal:
ssh login_id@hoffman2.idre.ucla.edu
where login_id is replaced by your cluster user name.

====GUI-Enabled SSH [Recommended]====
Macs (post - Snow Leopard 10.6.x) no longer come with a X Window System Server pre-installed.

'''Before doing the following steps, please install [http://xquartz.macosforge.org/ XQuartz] and restart your computer.'''

For more information about XQuartz, read [http://support.apple.com/kb/ht5293 here].
# Open up X11/XQuartz or Terminal. Both are under ''Applications > Utilities'' on Macs.
# Type the command
#: <pre>$ ssh -X [USERNAME]@hoffman2.idre.ucla.edu</pre>
#: filling in your Hoffman2 username.
#: The <code>-X</code> is for X11 Forwarding so that any graphics that are rendered on Hoffman2 get forwarded to the screen of your computer.
# Press enter and type in your password when it asks for it. No characters or asterisks will show up while you type.
# Provided your typing was good, you will be greeted by the Hoffman2 login message and have successfully SSH into a login node.

===Windows===
# Go [http://hpc.ucla.edu/hoffman2/access/access.php here] and follow the instructions under ''Windows''. We recommend PuTTY or Cgywin.
# Once you have that setup, the process is the same as if you were on a Mac or Linux/Unix machine
# TODO: [More information Coming]

==NX Client - GUI==
: ''The official description of how to do this is found [http://hpc.ucla.edu/hoffman2/access/nx.php here]''
The NX Client program allows you to set up a Virtual Network Computing (VNC)-like session with Hoffman2. This session will keep running even if your Internet connection drops in and out (much like [[Using Screen|screen]] on the command line).

===Mac OS X 10.7+ / Windows / Linux===
==== What You Need====
# Go to the No Machine website ([https://www.nomachine.com/download No Machine]) and download/install the No Machine for Mac OS X/Windows/Linux.
# Hoffman2 NX Client Public Key
#* To get the NX Client Public Key, follow the steps below or email support@ccn.ucla.edu
#** (OSX/Linux) Open up a Terminal and run the following command (replacing USERNAME with your Hoffman2 username)
#**:<code>$ scp USERNAME@hoffman2.idre.ucla.edu:/etc/nxserver/client.id_dsa.key ~/Documents/</code>
#** (Windows) Use a sftp program and download the file /etc/nxserver/client.id_dsa.key on Hoffman2 (hoffman2.idre.ucla.edu)

====Setup====
# Open up No Machine in Application/Desktop and Click Continue.
# A window titled "New Connection" will appear. Fill out the fields accordingly
#* Protocol -- SSH
#* Host -- "hoffman2.idre.ucla.edu"
#* Port -- 22

#* Select "Use the NoMachine login"
#* Select Alternate Server Key and (...) - and find the file (client.id_dsa.key) you downloaded earlier (in your Documents folder).
#* Don't use a proxy
#* Name -- Something like "Hoffman2"

# Double click on the connection you just created (it should be the only one in the list).
# Enter your Hoffman2 username and password and click "OK" (You may also check the box labeled "Save this setting in the configuration file" to avoid retyping this in the future)
# Select "Create a new session". or "New Virtual Desktop"
# In the next menu, select Create new '''GNOME''' virtual desktop.
# A virtual desktop should appear!

Reconnections in this client are not currently supported for Hoffman2, so please make sure to logout and close your connections properly. [http://hpc.ucla.edu/hoffman2/access/nx.php#logout]

====Troubleshooting====
If your NX Client session freezes and you are unable to close it properly, open ''NX Session Administrator'' and disconnect your session from there. This freezing often occurs when your Internet connection is lost abruptly. Another possible cause for freezing is scrolling on certain Windows touchpads.

For more Information [[http://hpc.ucla.edu/hoffman2/access/nx.php Hoffman2 NX Client]]

If you are unable to open Firefox ("Firefox is already running, but is not responding. To open a new window, you must first close the existing Firefox process, or restart your system."), deleting ~/.mozilla might fix the problem. ''Be warned:'' this will erase your profile, including bookmarks, history, saved passwords, etc! For instructions on backing up and restoring profile information, see [https://support.mozilla.org/en-US/kb/back-and-restore-information-firefox-profiles Mozilla Support].

== Change Passwords ==
Once you've logged on and made sure its works, you can change your password to something more rememberable
To change passwords, logon and type:
passwd
It should ask you for your old password and then new ones.

==External Links==
*[http://hpc.ucla.edu/hoffman2/access/access.php Hoffman2 Access]
*[http://hpc.ucla.edu/hoffman2/access/nx.php Hoffman2 via NX Client]
*[[Hoffman2:Accessing_the_Cluster-Historical_Notes | Historical Notes]]

Hoffman2:Accessing the Cluster

2014-11-19T17:43:39Z

Alhead: /* NX Client - GUI */

[[Hoffman2|Back to all things Hoffman2]]

Here are some of our favorite ways to access the Hoffman2 Cluster login nodes.

==SSH - Command Line==
SSH stands for ''Secure Shell'' and is a method of remotely logging into a computer using an encrypted connection. It is a command line tool and is available on most *nix-based operating systems with ports available for Windows.

===Mac/Linux/Unix===
====Simple SSH====
Use the ssh command from a terminal:
ssh login_id@hoffman2.idre.ucla.edu
where login_id is replaced by your cluster user name.

====GUI-Enabled SSH [Recommended]====
Macs (post - Snow Leopard 10.6.x) no longer come with a X Window System Server pre-installed.

'''Before doing the following steps, please install [http://xquartz.macosforge.org/ XQuartz] and restart your computer.'''

For more information about XQuartz, read [http://support.apple.com/kb/ht5293 here].
# Open up X11/XQuartz or Terminal. Both are under ''Applications > Utilities'' on Macs.
# Type the command
#: <pre>$ ssh -X [USERNAME]@hoffman2.idre.ucla.edu</pre>
#: filling in your Hoffman2 username.
#: The <code>-X</code> is for X11 Forwarding so that any graphics that are rendered on Hoffman2 get forwarded to the screen of your computer.
# Press enter and type in your password when it asks for it. No characters or asterisks will show up while you type.
# Provided your typing was good, you will be greeted by the Hoffman2 login message and have successfully SSH into a login node.

===Windows===
# Go [http://hpc.ucla.edu/hoffman2/access/access.php here] and follow the instructions under ''Windows''. We recommend PuTTY or Cgywin.
# Once you have that setup, the process is the same as if you were on a Mac or Linux/Unix machine
# TODO: [More information Coming]

==NX Client - GUI==
: ''The official description of how to do this is found [http://hpc.ucla.edu/hoffman2/access/nx.php here]''
The NX Client program allows you to set up a Virtual Network Computing (VNC)-like session with Hoffman2. This session will keep running even if your Internet connection drops in and out (much like [[Using Screen|screen]] on the command line).

===Mac OS X 10.7+ / Windows / Linux===
==== What You Need====
# Go to the No Machine website ([https://www.nomachine.com/download No Machine]) and download/install the No Machine for Mac OS X/Windows/Linux.
# Hoffman2 NX Client Public Key
#* To get the NX Client Public Key, follow the steps below or email support@ccn.ucla.edu
#** (OSX/Linux) Open up a Terminal and run the following command (replacing USERNAME with your Hoffman2 username)
#**:<code>$ scp USERNAME@hoffman2.idre.ucla.edu:/etc/nxserver/client.id_dsa.key ~/Documents/</code>
#** (Windows) Use a sftp program and download the file /etc/nxserver/client.id_dsa.key on Hoffman2 (hoffman2.idre.ucla.edu)

====Setup====
# Open up No Machine in Application/Desktop and Click Continue.
# A window titled "New Connection" will appear. Fill out the fields accordingly
#* Protocol -- SSH
#* Host -- "hoffman2.idre.ucla.edu"
#* Port -- 22

#* Select "Use the NoMachine login"
#* Select Alternate Server Key and (...) - and find the file (client.id_dsa.key) you downloaded earlier (in your Documents folder).
#* Don't use a proxy
#* Name -- Something like "Hoffman2"

# Double click on the connection you just created (it should be the only one in the list).
# Enter your Hoffman2 username and password and click "OK" (You may also check the box labeled "Save this setting in the configuration file" to avoid retyping this in the future)
# Select "Create a new session". or "New Virtual Desktop"
# In the next menu, select Create new '''GNOME''' virtual desktop.
# A virtual desktop should appear!

Reconnections in this client are not currently supported for Hoffman2, so please make sure to logout and close your connections properly. [http://hpc.ucla.edu/hoffman2/access/nx.php#logout]

====Troubleshooting====
If your NX Client session freezes and you are unable to close it properly, open ''NX Session Administrator'' and disconnect your session from there. This freezing often occurs when your Internet connection is lost abruptly. Another possible cause for freezing is scrolling on certain Windows touchpads.

For more Information [[http://hpc.ucla.edu/hoffman2/access/nx.php Hoffman2 NX Client]]

== Change Passwords ==
Once you've logged on and made sure its works, you can change your password to something more rememberable
To change passwords, logon and type:
passwd
It should ask you for your old password and then new ones.

==External Links==
*[http://hpc.ucla.edu/hoffman2/access/access.php Hoffman2 Access]
*[http://hpc.ucla.edu/hoffman2/access/nx.php Hoffman2 via NX Client]
*[[Hoffman2:Accessing_the_Cluster-Historical_Notes | Historical Notes]]

MR

2014-09-29T19:04:30Z

Alhead: /* Tutorials */ Added eternal link to the FSL tutorial

A collection of information about MR data from collection to processing/analysis.

==Collection==
How does one collect MR data?

===Staglin===
The [http://www.semel.ucla.edu/staglin Staglin IMHRO Center for Cognitive Neuroscience] is one of our main data collection facilities.
*[[StaglinCenter:MR]]

===EEG/FMRI===
Concurrent data collection of EEG and FMRI is possible at the Staglin Center.
*[[StaglinCenter:EEG-FMRI]]

===Transfer===
Data is automatically transferred from a DICOM server to our processing server ([[Hoffman2]]) nightly.

==Directory Structure==
Standards are important. And we've got standards about how our MR data should be kept.
*[[MR:DirectoryStructure]]

==Processing==
How to process MR data.

===Tutorials===
Some helpful tutorials about how to process MR data.

*[http://fsl.fmrib.ox.ac.uk/fslcourse/ FSL and FreeSurfer Course]

===Preprocessing===
Certain preprocessing steps are done to all data. This is facilitated by an automated script.
*[[MR:Processing:Preprocessing]]

===DTI===
*[[MR:Processing:DTI]]

Basic Preprocessing and ICA in EEGLAB

2013-04-16T23:32:48Z

Alhead: This page has no content, so I linked to the binica instructions.

Agatha will set up this page.

For now, see [[Hoffman2:MATLAB:EEGLAB#binica|ICA on Hoffman2]].

EEG Net Names

2013-04-09T01:48:32Z

Alhead: Typo

[[EEG|Back to all things EEG]]

Users can identify individual EEG nets by serial number or by nickname. In the interests of fun and science, the nets are named after constellations. The names for different categories of nets come from different constellation families.

==EEG Only==
These net names come from the Ursa Major family. Go Bruins!

*Cohen 54-56 cm: Ursa Minor

*Cohen 58-61 cm: Ursa Major

*Feusner 54-56 cm: Lynx

*Feusner 56-58 cm: Boötes

*Feusner 58-61 cm: Draco

==MR Safe==
These net names come from the signs of the zodiac.

*Older 54-56 cm: Gemini

*Older 56-58 cm: Libra

*Older 56-58 cm: Scorpio

*Newer 58-61 cm: Taurus

*Newer 58-61 cm: Cancer

==Modified MR Safe==
These net names come from the Orion family.

*54-56 cm: Lepus

*56-58 cm: Canis Minor

*56-58 cm: Canis Major

*56-58 cm: Orion

EEG Net Names

2013-04-09T01:41:36Z

Alhead: Added a link back to the main EEG page

[[EEG|Back to all things EEG]]

Users can identify individual EEG nets by serial number or by nickname. In the interests of fun and science, the nets are named after constellations. The names for different categories of nets come from different constellation families.

==EEG Only==
These net names come from the Ursa Major family. Go Bruins!

*Cohen 54-56 cm: Ursa Minor

*Cohen 58-61 cm: Ursa Major

*Feusner 54-56 cm: Lynx

*Feusner 56-58 cm: Boötes

*Feusner 58-61 cm: Draco

==MR Safe==
These net names come from the signs of the zodiac.

*Older 54-56 cm: Gemini

*Older 56-58 cm: Libra

*Older 56-58 cm: Scorpio

*Newer 58-61 cm: Taurus.

*Newer 58-61 cm: Cancer

==Modified MR Safe==
These net names come from the Orion family.

*54-56 cm: Lepus

*56-58 cm: Canis Minor

*56-58 cm: Canis Major

*56-58 cm: Orion

EEG

2013-04-09T01:37:56Z

Alhead: /* History */ Linked to the new page on EEG net names

A collection of information about EEG data from collection to processing/analysis.

==Collection==
How do you even get EEG data?

===Staglin===
The [http://www.semel.ucla.edu/staglin Staglin IMHRO Center for Cognitive Neuroscience] is our main EEG data collection facility. Go here to learn how data collection works at the Staglin Center.
*[[StaglinCenter:EEG]]

===EEG/FMRI===
Concurrent data collection of EEG and FMRI is possible at the Staglin Center.
*[[StaglinCenter:EEG-FMRI]]

===Transfer===
For now you have to move data by sneaker-net from the acquisition computers to your computer. We may automate this process in the future.

==Directory Structure==
Standards are important. And we're hoping to have standards about how our EEG data is kept?
*[[EEG:DirectoryStructure]]

==Processing==
How to process EEG data.

===Preprocessing===
Certain preprocessing steps should be done to all data.
*[[EEG:Processing:Preprocessing]]

===ICA===
Independent Component Analysis
*[[EEG:Processing:ICA]]

===Source===
Source localization.
*[[EEG:Processing:Source]]

Under construction
*[[Basic Preprocessing in NetStation]]
*[[Basic Preprocessing and ICA in EEGLAB]]
*[[Time-Frequency Analyses - Matlab/EEGLAB]]
*[[Source Analysis]]
*[[Machine Learning]]

== History ==

*[[EEG fMRI noise 2011]]
*[[EEG Net Names]]

EEG Net Names

2013-04-09T01:36:51Z

Alhead: Formatting change

Users can identify individual EEG nets by serial number or by nickname. In the interests of fun and science, the nets are named after constellations. The names for different categories of nets come from different constellation families.

==EEG Only==
These net names come from the Ursa Major family. Go Bruins!

*Cohen 54-56 cm: Ursa Minor

*Cohen 58-61 cm: Ursa Major

*Feusner 54-56 cm: Lynx

*Feusner 56-58 cm: Boötes

*Feusner 58-61 cm: Draco

==MR Safe==
These net names come from the signs of the zodiac.

*Older 54-56 cm: Gemini

*Older 56-58 cm: Libra

*Older 56-58 cm: Scorpio

*Newer 58-61 cm: Taurus.

*Newer 58-61 cm: Cancer

==Modified MR Safe==
These net names come from the Orion family.

*54-56 cm: Lepus

*56-58 cm: Canis Minor

*56-58 cm: Canis Major

*56-58 cm: Orion

EEG Net Names

2013-04-09T01:35:10Z

Alhead: Created a page listing the net sizes along with their individual nicknames.

Users can identify individual EEG nets by serial number or by nickname. In the interests of fun and science, the nets are named after constellations. The names for different categories of nets come from different constellation families.

==EEG Only==
These net names come from the Ursa Major family. Go Bruins!

Cohen 54-56 cm: Ursa Minor

Cohen 58-61 cm: Ursa Major

Feusner 54-56 cm: Lynx

Feusner 56-58 cm: Boötes

Feusner 58-61 cm: Draco

==MR Safe==
These net names come from the signs of the zodiac.

Older 54-56 cm: Gemini

Older 56-58 cm: Libra

Older 56-58 cm: Scorpio

Newer 58-61 cm: Taurus.

Newer 58-61 cm: Cancer

==Modified MR Safe==
These net names come from the Orion family.

54-56 cm: Lepus

56-58 cm: Canis Minor

56-58 cm: Canis Major

56-58 cm: Orion

Hoffman2:MATLAB:EEGLAB

2013-03-12T03:20:59Z

Alhead: Changed the recommended 12 hours for ICA to 8 hours. This should still be plenty of extra time: my 25-minute recordings finished in under 5 hours.

[[Hoffman2|Back to all things Hoffman2]]

[[Hoffman2:MATLAB|Back to all things MATLAB]]

The three of the most recent versions of EEGLAB are maintained on Hoffman2 for the FMRI group in the directory
/u/home/FMRI/apps/eeglab

==Adding EEGLAB to your MATLAB path==
Choose one of the versions from
/u/home/FMRI/apps/eeglab
and add it to your MATLAB path by doing.

# [[Hoffman2:MATLAB#GUI|Start MATLAB on Hoffman2]]
# Go to
#: ''"File"'' > ''"Set Path..."''
#* Click ''"Add with Subfolders..."''
#* Navigate to
#*: <pre>/u/home/FMRI/apps/eeglab</pre>
#*: choose which version you'd like to use and click on it.
#* Click ''"Ok"''
#* To save this for future sessions, click ''"Save."''
#* If you don't want to save this path, click ''"Close"'' and then click ''"No"'' on the window that pops up.
# Go to the MATLAB command line and start EEGLAB by typing
#: <pre>>> eeglab</pre>

==CIDAR ADHD==
For steps on how to process CIDAR data in EEGLAB, [[Hoffman2:MATLAB:EEGLAB:CIDAR|click here]].

==binica==
If you want to run ICA decomposition on your data, it can often be a very time-intensive process. Doing this through the EEGLAB GUI (runica) is almost an order of magnitude slower than doing it with <code>binica</code> or via command line. So let's walk through how to do this the fastest (most parallelizable) way by submitting jobs on Hoffman2.

===Export your data from NetStation===
# If you are going to preprocess your data in NetStation, do so first.
# Export your data in the '''NetStation simple binary''' format which produces files with the ''.raw'' extension. [[Hoffman2:Data Transfer|Upload this to Hoffman2 by your choice method]].

===Prep your data for ICA===
# [[Hoffman2:MATLAB|Start up MATLAB on Hoffman2]] and start EEGLAB
# Go to
#: ''"File"'' > ''"Import data"'' > ''"From Netstation binary simple file"''
#* Find your ''.raw'' file and select it.
#* Click ''"Ok"'' on the first pop up window, and in the second give your dataset a name before clicking ''"Ok.""
# When EEGLAB finishes importing your data ''Done'' will appear above the command line.
# At this time, do any preprocessing you'd like on the data in EEGLAB/MATLAB.
# Add this special directory to your MATLAB path,
#: <pre>>> addpath('/u/home/FMRI/apps/examples/binica');</pre>
# Use the command,
#: <pre>>> prep4binica(ALLEEG.data, ALLEEG.nbchan, ALLEEG.trials*ALLEEG.pnts, 'verbose', 'on', 'filenum', FILENAME);</pre>
# This will save out the necessary files to run ICA:
#* data in a float-point file, ''.fdt''
#* parameters for ICA in a configuration file, ''.sc''
# Exit out of EEGLAB (''"File"'' > ''"Quit"'').
# Exit out of MATLAB

===Run ICA===
If you prepared multiple datasets for ICA, you could submit many jobs in parallel to speed up the processing time.
# Use a [[Text Editors|text editor]] to make a script (e.g. icaScript.sh) on Hoffman2 with the following contents
#: <pre>#!/bin/bash
/u/home/FMRI/apps/eeglab/current/functions/resources/ica_linux < path/to/sc/file </pre>
#: where you replace '''/path/to/sc/file''' with the full path to the ''.sc'' file created by <code>prep4binica</code>.
# Make the script executable
#: <pre>chmod 750 /path/to/script</pre>
#: replacing '''/path/to/script''' with the path to your script file.
# [[Hoffman2:Submitting Jobs|Submit this script as a job]], we recommend demanding at least 8 hours (<code>time=8:00:00</code>) and 2GB of RAM (<code>mem=2048M</code>) for your job.
# Wait for the script to complete.

===Import ICA data back to EEGLAB===
# [[Hoffman2:MATLAB|Start up MATLAB on Hoffman2]] and start EEGLAB
# Go to
#: ''"File"'' > ''"Import data"'' > ''"From Netstation binary simple file"''
#* Find your ''.raw'' file and select it.
#* Click ''"Ok"'' on the first pop up window, and in the second give your dataset a name before clicking ''"Ok.""
# When EEGLAB finishes importing your data ''Done'' will appear above the command line.
# Go to
#: ''"Edit"'' > ''"Dataset into"''
#* Click ''"Browse"'' next to ''"ICA weights array or text/binary file (if any):"'' and find the ICA weight file (''.wts'' extension).
#* Click ''"Browse"'' next to ''"ICA sphere array or text/binary file (if any):"'' and find the ICA sphere file (''.sph'' extension).
#* Click ''"Ok"''.
# You should now be able to view the ICA information within EEGLAB.

==Only Using EGI's "Good" Segments in EEGLAB==
NetStation preprocessing has built in methods of classifying data segments as "good" or "bad" depending on a variety of criteria related to noise measurements. Please refer to their pertinent documentation to understand how this is done. In the case where you do your preprocessing in NetStation but would like to use EEGLAB's ICA tool, you probably don't want all those "bad" segments to be used for ICA calculations or other work.

Sadly, your only options for exporting only the "good" segments from NetStation directly to MATLAB is in the form of a ''.mat'' file. '''But EEGLAB doesn't play nicely with these files!'''

In comes the tedious translation process to make your data usable...
# Export your preprocessed data from NetStation as a "Net Station Simple Binary" file.
#: '''Do not export them as "Net Station Simple Binary (Ignore Events)"'''
#: '''Do not export them as "Net Station Simple Binary (Epoch Marked)"'''
# Import the data file into EEGLAB
# Open NetStation, and in the top menu bar go to ''"Tools"'' > ''"Browse Files..."'' which will open a new data explorer window.
# In Finder, locate your final preprocessed data (the one that you ran the Export tool on earlier).
# Drag this file into the left had bar labeled ''"Source Files."''
# In the top right area of the window, click on the ''"Categories and Subjects"'' tab and you should see a grid of numbers and labels.
#: The segment types will have their labels at the beginning of each row (e.g. Belief, Disbelief)
#: Each source file will have a dedicated column labeled with something (I believe it to be the subject linked to the recording).
# Click on the first segment type label and in the bottom right area of the window you will see a list of all segments of that type.
# If you click on the column label ''"Time"'' it will order the segments chronologically which is the same way they are ordered when you export them as a "Net Station Simple Binary" file.
# Back in EEGLAB, use the menu to go to ''"Edit"'' > ''"Select data"'' which opens another window.
#: In this window, you can use different criteria for selecting portions of data. The method pertinent here is by ''"Epoch range."''
#: I would recommend clicking the little check box to the right of the input box for ''"Epoch range"'' so you only have to specify which epochs you want removed. '''There should be fewer epochs to remove than there are epochs you want to keep...otherwise your data is really messy and using it might not be recommended...'''
# Have fun counting your way down the lines of the NetStation File Browser to determine exactly which segments are "bad."
# Say the sixth segment of the first category is bad (these are the ones with a red circle and line through them at the beginning of the line instead of a green circle). In the EEGLAB data selection window, you need to add ''"6"'' to the ''"Epoch range"'' input box.
# Once you've gone through and told EEGLAB all the epochs you want removed, click the ''"Ok"'' button and it will start making a new dataset.
# Run [[Hoffman2:MATLAB:EEGLAB#Prep_your_data_for_ICA|prep4binica]] on the resulting dataset.

===Pro Tip===
If you have two or more types of segments in NetStation, counting and adding can be a dangerous game. So make use of MATLAB to simplify things.

e.g.
* You have two segment types: B and D
* There are 40 type B segments, of which Net Station claims only 37 are good.
* There are 60 type D segments, of which Net Station claims only 50 are good.
* In the EEGLAB ''"Select data"'' window, you make sure to click the check box to the right of the ''"Epoch range"'' input box so that you only have to list the epochs you want removed from the dataset.
* In the NetStation you click on the "B" category and scrolling through the segments you find that segments 1, 21, and 37 have the little red crossed circle indicating they are bad.
* In the EEGLAB ''"Select data"'' window's ''"Epoch range"'' input box you type
1 21 37
* In the NetStation you then click on the "D" category (since it would be the second category). Scrolling through the segments you find that the 40th through the 49th listed segments all have the red crossed circle indicating they are bad.
* In the EEGLAB ''"Select data"'' window's ''"Epoch range"'' input box, you then edit it to read
1 21 37 40+[40:49]
* This will work because MATLAB is going to process these numbers and see
1 21 37 80 81 82 83 84 85 86 87 88 89
* The "40+[" part is important because the first "D" category segment is actually the 41st segment overall. If you have more than two categories, you'd have to do similar arithmetic to properly indicate which epochs you want removed.

Happy counting.

==External Links==
*[http://sccn.ucsd.edu/eeglab/allfunctions/binica.html binica]
*[http://sccn.ucsd.edu/wiki/A01:_Importing_Continuous_and_Epoched_Data#Importing_Netstation.2FEGI_files What type of EGI files EEGLAB understands]

Hoffman2:Compiling MATLAB

2013-03-06T01:40:01Z

Alhead: added a line for loading modules prior to calling "module load matlab"

[[Hoffman2|Back to all things Hoffman2]]

Running the MATLAB GUI is not always desirable. If you already know that your code works and no visuals or user interaction are needed, then using the MATLAB GUI is unnecessary and adds extra work for the computer. Instead, it may be better to compile your MATLAB code into an executable that can be submitted as a job on Hoffman2.

Furthermore, if you need to run the same MATLAB script on multiple subjects and would like to do so in parallel, you will find that you can't simply open up multiple instances of MATLAB on Hoffman2. This is because each user is only allotted one MATLAB license. To parallelize your processing, it would be better to compile your MATLAB script and submit a job for each subject using the compiled code. '''Compiled code does not require a MATLAB license in order to run.'''

==Version Notice - 2012.04.23==
'''As of 2012.04.23 ATS updated the default MATLAB version from 7.11 (R2010b) to 7.14 (R2012a).'''

This means that any MATLAB code previously compiled will need to load the old MATLAB module in order to run. e.g.
$ module load matlab/7.11
$ /path/to/my/old/compiled/code

And the <code>matexe.q</code> tool will be using the newer MATLAB module. Which means you can't use it to submit previously compiled code. Please recompile your code to work with the new MATLAB version before submitting jobs with this tool.

==Compiling==
There is a handy tool, <code>mcc</code>, which can take a MATLAB .m file and compile it into an executable that can be run outside of MATLAB. It is expensive to buy, but luckily Hoffman2 has already done the purchasing for you.

'''Remember that to use <code>mcc</code>, you need an open MATLAB license. If you are running MATLAB already and open up a new Hoffman2 session intending to compile something with <code>mcc</code>, know that you will see errors and compilation will fail because you are already using your one allotted MATLAB license.'''

We have two example MATLAB scripts:

'''/u/home/FMRI/apps/examples/mcc/subfunctions/exampleSubfunction.m'''

This function can take any number of arguments and the text it prints out is based on the type of variables it receives. It is kept in a separate directory from the exampleMatlabScript.m file to illustrate how to work with dependent files in different parts of the filesystem.

function exampleSubfunction(varargin)

fprintf('This is a MATLAB function that takes input arguments.\n');

for i=1:length(varargin)
if( ~isempty(varargin{i}) )
switch class(varargin{i})
case 'double'
fprintf('Argument #%d\t -- %s -- is a double\n', i, varargin{i});
case 'char'
fprintf('Argument #%d\t -- %s -- is a char\n', i, varargin{i});
otherwise
fprintf('Argument #%d\t -- is an unknown\n', i);
end
else
fprintf('Argument #%d\t -- is empty\n', i);
end
end
end

'''/u/home/FMRI/apps/examples/mcc/exampleMatlabScript.m'''

Makes use of the exampleSubfunction() function.
function matlabScript(varargin)

fprintf('Passing numbers to the subfunction...\n');
subfunction(1, 2, 3);

fprintf('Passing characters to the subfunction...\n');
subfunction('a', 'b', 'c');

fprintf('Passing whatever arguments you gave me on to the subfunction...\n');
for i=1:length(varargin)
subfunction(varargin{i});
end

end

To compile this example script, first [[Hoffman2:Interactive Sessions|check out an interactive node]] '''because this can be a computational intensive process'''. Then run the following commands
$ mkdir ~/mccExample
$ cd ~/mccExample
$ mcc -m /u/home/FMRI/apps/examples/mcc/exampleMatlabScript.m -R -singleCompThread -I /u/home/FMRI/apps/examples/mcc/subfunctions

; <code>-m /u/home/FMRI/apps/examples/mcc/exampleMatlabScript.m</code>
: This flag is used to indicate which file is to be compiled.
; <code>-R -singleCompThread</code>
: This flag indicates what resources are needed. Default is to ask for all available cores, but by only requesting a single core you allow yourself more flexibility. If your code needed all the cores on a node, any jobs you submit to the queue will probably wait much longer to execute. If your code only needs one core, you job can be more flexible in scheduling and will probably execute sooner.
; <code>-I /u/home/FMRI/apps/examples/mcc/subfunctions</code>
: This flag is used to indicate the subdirectories where any support files are located so that they can be included in the compiling. If you had support .m files in multiple directories, you would need to include each separately e.g.
:: <pre>mcc -m /path/to/main/file -R -singleCompThread -I /path/to/file/one -I /path/to/file/two -I /path/to/file/three</pre>

The output will probably start with
Ifconfig uses the ioctl access method to get the full address information, which limits hardware addresses to 8 bytes.
Because Infiniband address has 20 bytes, only the first 8 bytes are displayed correctly.
Ifconfig is obsolete! For replacement check ip.
which can be ignored and will be followed by any other messages related to the compiling, or error messages if something went wrong.

==Testing==
Now that you've compiled your code, you should test it to make sure it works before submitting 100,000 jobs using it.

# [[Hoffman2:Interactive Sessions|Check out an interactive node]]
# Execute
#: <pre>$ module load matlab</pre>
#: so that the computing node knows how to speak MATLAB
# Then change to the directory where the compiled code is
#: <pre>$ cd ~/mccExample</pre>
# And run your compiled code
#: <pre>$ ./exampleMatlabScript </pre>
#: Feel free to add any arguments to your function call, e.g.
#: <pre>$ ./exampleMatlabScript ARG1 2 3 4</pre>
#: to see how the output changes.

==Submitting==
You've compiled code and tested that it works. Time to submit it as a job.

===matexe.q===
ATS has a tool for this (similar to [[Hoffman2:Submitting Jobs#job.q|job.q]]) called <code>matexe.q</code>. It's a step-by-step tool that's pretty self explanatory, but we provided an example anyway.

====Example====
# Once on Hoffman2, you'll need to edit one file so pull out your favorite [[Text Editors|text editor]] and edit the file
#: <pre>~/.queuerc</pre>
# Add the line (if it isn't already there)
#: <pre>set qqodir = ~/job-output</pre>
# You've just set the default directory where your job command files will be created. Save the configuration file and close your text editor.
# Make that directory using the command
#: <pre>$ mkdir ~/job-output</pre>
# Now run
#:<pre>$ matexe.q</pre>
# Press enter to acknowledge any messages that may appear (READ IT FIRST THOUGH).
# Type ''Build <ENTER>'' to begin creating an SGE command file.
# The program now asks you which script you'd like to run, enter the following text to use our example script
#: <pre>~/mccExample/exampleMatlabScript</pre>
# The program now asks how much memory the job will need (in [http://en.wikipedia.org/wiki/Megabyte Megabytes]). This script is really simple, but let's go with the default 1024.
# The program now asks how long will the job take (in hours). Go with the minimum 1 hour; it will complete in much less than this.
# The program now asks if your job should be limited to only your resource group's cores. Answer ''n'' because you do not need to be limiting yourself here and the job is not going to be running for more than 24 hours.
# It will ask for any arguments you'd like to supply. Feel free to put random values here or nothing at all to see how the example script treats your arguments.
# Soon, the program will tell you that ''exampleMatlabScript.cmd'' has been built and saved.
# When it asks you if you would like to submit your job, say no. Then type ''Quit <ENTER>'' to leave the program.
# Now you should be able to run
#: <pre>$ ls ~/job-output</pre>
#: and see ''exampleMatlabScript.cmd''. This file will stay there until you delete it and can be run over and over again. Making a command file like this is especially useful if there is a task you'll be running repeatedly on Hoffman2. But if this is something you only need to run once, you should delete the file so you don't needlessly approach your [[Hoffman2:Quotas|quota]].
# The time has come to actually run the program (thought we'd never get to that, didn't you?). Type
#: <pre>$ qsub job-output/exampleMatlabScript.cmd</pre>
#: and after hitting enter, a message similar to this will pop up:
#: <pre>Your job 1882940 ("exampleMatlabScript.cmd") has been submitted</pre>
#: where the number is your JobID, a unique numerical identifier for the computer job you have submitted to the queue.
# Now you can check if the job has finished running by doing
#: <pre>$ ls ~/job-output</pre>
# When two files named ''exampleMatlabScript.output.[JOBID]'' and ''exampleMatlabScript.joblog.[JOBID]'' (where JOBID is your job's unique identifier) appear, your job has run.
#: ''exampleMatlabScript.output.[JOBID]''
#:: This file has all the standard output generated by your script. In this case it will be something like
#::: <code>Passing numbers to the subfunction...</code>
#::: <code>This is a MATLAB function that takes input arguments.</code>
#::: <code>Argument #1 -- -- is a double</code>
#::: <code>Argument #2 -- -- is a double</code>
#::: <code>Argument #3 -- -- is a double</code>
#::: <code>Passing characters to the subfunction...</code>
#::: <code>This is a MATLAB function that takes input arguments.</code>
#::: <code>Argument #1 -- a -- is a char</code>
#::: <code>Argument #2 -- b -- is a char</code>
#::: <code>Argument #3 -- c -- is a char</code>
#::: <code>Passing whatever arguments you gave me on to the subfunction...</code>
#::: <code>This is a MATLAB function that takes input arguments.</code>
#::: <code>Argument #1 -- 1 -- is a char</code>
#::: <code>This is a MATLAB function that takes input arguments.</code>
#::: <code>Argument #1 -- a -- is a char</code>
#::: <code>This is a MATLAB function that takes input arguments.</code>
#::: <code>Argument #1 -- 2 -- is a char</code>
#::: <code>This is a MATLAB function that takes input arguments.</code>
#::: <code>Argument #1 -- b -- is a char</code>
#::: <code>This is a MATLAB function that takes input arguments.</code>
#::: <code>Argument #1 -- 3 -- is a char</code>
#::: <code>This is a MATLAB function that takes input arguments.</code>
#::: <code>Argument #1 -- c -- is a char</code>
#::: <code>Warning: No display specified. You will not be able to display graphics on the screen.</code>
#: ''exampleMatlabScript.joblog.[JOBID]''
#:: This file has all the details about when, where, and how your job was processed. Useful information if you are going to be running this job over and over and need to fine tune the resources it uses.
# Better ways of checking on your job can be found [[Hoffman2:Monitoring Jobs|here]].
# Finally, go check the inbox of the email you used to sign up for your Hoffman2 account. There will be two emails from "root@mail.hoffman2.idre.ucla.edu" that indicate when the job was started and when the job was completed. This is one of the neat features of the queue so that you can be alerted about the progress of your job without having to stay logged into Hoffman2 and checking on it constantly.

===By hand===
You could also make a shell script that contains
#!/bin/bash
source /u/local/Modules/default/init/modules.sh
module load matlab
/path/to/compiled/matlab/script
and submit this shell script using [[Hoffman2:Submitting Jobs#qsub|qsub]] or [[Hoffman2:Submitting Jobs#q.sh|q.sh]] to achieve similar results.

==About those arguments==
If you played around with submitting different arguments to the sample script we compiled above, you will have noticed that '''compiled MATLAB treats all arguments as if they are strings.''' So if you plan to leverage arguments in your code to make your functions more useful, and we recommend that you do, you may need to make use of the command
str2num()
to convert certain arguments into usable numbers.

==Known Issues==
* The official mcc documentation cites a <code>-a</code> flag for including a directory and all of its subdirectories recursively. We haven't found this flag to work very effectively and strongly suggest you use <code>-I</code> to explicitly name all the directories that have .m files your code depends on.
* Compiling EEGLAB has thus far failed on Hoffman2. Compiling SPM5 or SPM8 may fail similarly. If you figure out how to do this, let us know.
* You cannot compile something while you have another MATLAB session open. Each Hoffman2 user is allotted one MATLAB license at a time, and <code>mcc</code> requires a license to run.

==External Links==
*[http://www.mathworks.com/support/solutions/en/data/1-18448/?solution=1-18448 How to pass variables to compiled MATLAB code]

Principles of Neuroimaging B - 2012

2012-03-07T22:25:22Z

Alhead: /* Friday 3/9/12 - TOPIC. "Speaker" */ Added handout pdf

=Principles of Neuroimaging B, Winter, 2012 - Class Schedule and Syllabus=

:'''[[Principles_of_Neuroimaging_-_2011-2012 | Main course page for Principles of Neuroimaging (2010-11)]]'''

:'''[[Principles_of_Neuroimaging_A_-_2011 | M284A Principles of Neuroimaging A]]'''

*[[Notes for Instructors]]

=Lecture Videos=
*[[Media:1_3_11_mark_cohen_mri.mp4|Friday 1-3-11 - MR Signals and Contrast, Speaker Mark Cohen]]
*[[Media:1_5_11_mark_cohen_mri_p1.mp4|Wednesday 1-5-11 - MR Spatial Encoding I, Speaker Mark Cohen]]
*[[Media:1_5_11_mark_cohen_mri_p2.mov|Wednesday 1-5-11 - MR Spatial Encoding II, Speaker Mark Cohen]]
*[[Media:1_10_11_mark_cohen_mri.mp4|Friday 1-10-11 - fMRI and Diffusion, Speaker Mark Cohen]]
*[[Media:1_12_11_mark_cohen_mri.mp4|Wednesday 1-12-11 - fMRI Image Quality and Artifacts, Speaker Mark Cohen]]
*[[Media:1_24_11_susan_bookheimer_exp_design_p1.mp4|Friday 1-24-11 - Experimental Design I, Speaker Susan Bookheimer]]
*[[Media:1_24_11_susan_bookheimer_exp_design_p2.mov|Friday 1-24-11 - Experimental Design II, Speaker Susan Bookheimer]]
*[[Media:1_26_11_nathan_hageman_dti.mp4|Wednesday 1-26-11 - DTI, Speaker Nathan Hageman]]
*[[Media:1_31_11_gregory_simpson_meg_eeg.mp4|Friday 1-31-11 - MEG/EEG, Speaker Gregory Simpson]]
*[[Media:2_2_11_low_field_mri.mp4|Wednesday 2-2-11 - Ultra Low Field MRI, Speaker Konstantin Penanen]]
*[[Media:2_9_11_allan_wu_tms.mp4|Wednesday 2-9-11 - TMS, Speaker Allan Wu]]
*[[Media:2_14_11_jeff_algers_mrs.mp4|Friday 2-14-11 - MRS, Speaker Jeff Algers]]

=Week 1 Magnetic Resonance Imaging=
Magnetic Resonance Imaging (MRI) is probably the most influential and most felxible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies

==''Wednesday 1/11/12'' - MRI. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
''Required Readings''
:*[[media:MRIforPNIB.pdf‎ | MRI Slides]]
:*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.
:*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource
:*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']
[[Image:HahnFig1.png]]
''above'': Figure 1 from Hahn, 1950

''Suggested Further Reading''
[[image:PSatSeq.jpg|right]]

==''Friday 1/13/12'' - MRI II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
''Required Readings''
:*[[media:MRIforPNIB.pdf‎ | MRI Slides (same as 1/4/12)]]

''Suggested Further Reading''
:*READING

:*[[media:PS1-PNIB2011.pdf | Problem Set 1]]

WEEKLY SUMMARY

=Week 2 MRI Applications=

==''Wednesday 1/18/12'' - Connectivity. ''Speaker'': [http://ccn.ucla.edu/~jbrown/ Jesse Brown]==
OUTLINE
''Required Readings''
:*

''Suggested Further Reading''
:*[[Media:DTIHageman.pdf | Hageman DTI Slides]]
:*[[Media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]
:*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]

:Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):
:*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]
:*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]

''Suggested Further Reading''
:*READING

==''Friday 1/20/12'' - Advanced MRI Pulse Sequences. ''Speaker'': [http://www.radiology.ucla.edu/dcvi/html/people/Ennis.html Daniel Ennis]==

=Week 3 Advanced MRI Applications and TMS=

==''Wednesday 1/25/12'' - Diffusion. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=45540 Jeffry Alger]==
OUTLINE
[[image:Bandwidth.jpg|right]]
''Required Readings''
:*[[media:ALGER_PrinciplesNeuroImaging2012DTI.pdf‎ | DTI lecture notes]]
:*[[media:Alger_PrinciplesNeuroImaging2012MRS.pdf‎ | Spectroscopy lecture notes.]]
'Suggested Readings''

:*[http://www.intechopen.com/source/pdfs/28790/InTech-Diffusion_tensor_imaging_structural_connectivity_insights_limitations_and_future_directions.pdf DTI basics and future directions]

==''Friday 1/27/12'' - TMS (tentative). ''Speakers'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu], ==
Transcranial Magnetostimulation is fundamentally different than the other technologies we have explored, in that it is used specifically to ''alter'' ongoing brain activity. While not exactly an imaging method, the TMS instrument is image-guided and uses tomographic placement.

'Required Readings''
:* [[media:TMS_Wu_2011.pdf | Wu 2011 Lecture slides]]
:* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]
:* [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T0J-50CV801-1&_user=4423&_coverDate=01%2F31%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000059605&_version=1&_urlVersion=0&_userid=4423&md5=f9fa3c7d63942dfb3c74e047a1f848bc&searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]

''Suggested Further Reading''

:* [[media:WuTMS-05-04-10.pdf | Handout for Wu TMS Lecture, 2010]]

Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:
:*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]

=Week 4 PET=
==''Wednesday 2/1/12'' - Positron Emission Tomography (PET). ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]==
OUTLINE
[[image:ParallaxError.jpg|right]]
''Required Readings''
:*[[media:PET_2010.pdf | PET Imaging handout]]

''Suggested Further Reading''
:*READING

==''Friday 2/3/12''- Positron Emission Tomography (PET) Applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]==
OUTLINE
[[image:SmokerStroop.png|right]]
''Required Readings''
:*[[media:PET_applications2-08-12SM.pdf‎| PET Applications handout]]
:* [http://www.ncbi.nlm.nih.gov/pubmed/3099392?dopt=Citation “Mapping human brain monoamine oxidase A and B with 11C-labeled suicide inactivators and PET.” Science, 235(4787): p. 481-485. 1987.]
:* [[media:MukherjeeRadiopharmaceuticals.pdf | Mukherjee: Radiopharmaceuticals for Brain Imaging]]
:* [[media:Martinez_Drugs_of_Abuse.pdf | Imaging Neurotransmitter Release by Drugs of Abuse, Diana Martinez and Rajesh Narendran]]

''Suggested Further Reading''
:*n/a

=Week 5 fMRI and Ultrasound=
==''Wednesday 2/8/12'' - Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
''Required Readings''
:*[[media:MultiModalNITP2012SM.pdf‎ | Multimodal imaging handout]]

==''Friday 2/10/12'' - Ultrasound (''tentative''). ''Speaker'': [http://casit.ucla.edu/body.cfm?id=129 Martin Culjat]==
OUTLINE

Ultrasound is one of the earliest means of seeing into the body. Until recently, however, seeing into the brain has been very poor. Recent advances are improving on this.

''Required Readings''
:*

''Suggested Further Reading''
:*[http://www.jultrasoundmed.org/content/24/12/1671.full.pdf+html “Intraoperative sonography for neurosurgery.” J Ultrasound Med, 24(12): p. 1671-1682. 2005
]
:*[http://folk.ntnu.no/htorp/Undervisning/MEDT8002/litteratur/NURO51020402.pdf Brain operations guided by real-time two-dimensional ultrasound: new possibilities as a result of improved image quality.” Neurosurgery, 51(2): p. 402-411; discussion 411-402. 2002]
:*[[media:biomed298 | Biomed 298 Design of Medical Ultrasound]]

=Week 6 =

==Wednesday 2/15/12 - Connectivity. "Jesse Brown"==
OUTLINE 
Connectivity in neuroimaging is a broad subject. These slides focus on resting state fMRI and DTI based connectivity methods and results.
[[Media:nitp_connectivity_02142012.pdf]]

''Required Readings''
:*[[media:Bullmore_Sporns_NatRevNeuro_2009.pdf | Review of connectivity]]

''Suggested Further Reading''
:*Networks of the Brain by Olaf Sporns

''Links of interest''
:*[http://fcon_1000.projects.nitrc.org/ INDI]: the International Neuroimaging Data-sharing Initiative. A very useful source of publicly available fMRI and DTI data.
:*[http://www.humanconnectome.org/ Human Connectome Project]: The WashU-UMinn consortium will scan 1200 individuals with resting state fMRI, DSI, and structural MRI, along with MEG and 7-Tesla scanning in some cases.
:*[http://umcd.humanconnectomeproject.org/ UMCD]: The UCLA Multimodal Connectivity Database, a web-based repository for brain network analysis and data sharing.

==Friday 2/17/12 - Brain Stimulation. "Alexander Bystritsky"==
OUTLINE
''Required Readings''

[[media:Brainstimulation2012AB.pdf | Brain Stimulation]]

''Suggested Further Reading''
:*READING

=Week 7 =

==Wednesday 2/22/12 - Methods of Dimension Reduction. "Ariana Anderson"==
OUTLINE
''Required Readings''

''Suggested Further Reading''
:*READING

==Friday 2/25/12 - Bayesian Statistics. "Donatello Telesca"==
OUTLINE
''Required Readings''

''Suggested Further Reading''
:*READING

=Week 8 =

==Wednesday 2/29/12 - CLASS IS CANCELLED FOR TODAY. SORRY==

==Friday 3/2/12 - TOPIC. "Speaker"==
OUTLINE
''Required Readings''

''Suggested Further Reading''
:*READING

=Week 9 =

==Wednesday 3/7/12 - TOPIC. "Speaker"==
OUTLINE
''Required Readings''

''Suggested Further Reading''
:*READING

==Friday 3/9/12 - TOPIC. "Speaker"==
OUTLINE
Compressed sensing lecture by Dr. Kevin Kelly of Rice University.

''Required Readings''
*[[media:Compressed_imaging_tutorial.pdf | Compressed imaging handout]]

''Suggested Further Reading''
:*READING

=Week 10 =

==Wednesday 3/14/12 - TOPIC. "Speaker"==
OUTLINE
''Required Readings''

''Suggested Further Reading''
:*READING

==Friday 3/16/12 - TOPIC. "Speaker"==
OUTLINE
''Required Readings''

''Suggested Further Reading''
:*READING

=FINALS=
3/19-23/12

==''Friday 1//12'' - fMRI. ''Speaker'':
[http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
''Required Readings''
:*[http://www.brainmapping.org/NITP/PNA/Readings/MRIforNITP.pdf slides (same as 1/3/12)]

''Suggested Further Reading''
:*READING

Dr. Simpson is a leading expert in the use of scalp electrophysiology (EEG and MEG) to explore the dynamical processes of the human brain, and the integration of activity across cortex in complex human behaviors. Notably, the MEG instrument also uses the SQUID technology

Konstantin Penanen, together with Inseob Hahn and Byeong Ho Eom, have created a highly unusual MR imaging instrument that collects data in a magnetic field less than that of the earth. The tool uses '''S'''uperconductin '''QU'''antum '''I'''nterference '''D'''evices (SQUIDs) that detect the magnetic resonance imaging signal by direct magnetometry, rather than by induction.

==''Friday 1/31/12'' - MEG and EEG. ''Speaker'': [http://www.labome.org/expert/usa/university/simpson/gregory-v-simpson-1030707.html Greg Simpson]==
[http://books.google.com/books?id=_UXLRzqrkrQC&pg=PA26&lpg=PA26&dq=greg+simpson+eeg&source=bl&ots=3w1w34NL5x&sig=M7mdZRODLpmSpqnsnLkioBGcEQo&hl=en&ei=hT6eTP_2GJHksQPu_JXWAQ&sa=X&oi=book_result&ct=result&resnum=2&ved=0CBYQ6AEwAQ#v=onepage&q=greg%20simpson%20eeg&f=false A story]

Suggested Reading

[http://www.ncbi.nlm.nih.gov/pubmed/18701689?dopt=Citation J Neurosci. 2008 Aug 13;28(33):8268-72. "Very slow EEG fluctuations predict the dynamics of stimulus detection and oscillation amplitudes in humans". Monto S, Palva S, Voipio J, Palva JM.]

==''Friday 2/2//12'' - Ultralow field MRI. ''Speaker'': '''Konstantin Penanen''' NASA/CalTech Jet Propulsion Laboratory==
OUTLINE
[[image:miniscanGB.jpg|right]]

* [[media:Penanen_UCLA_Neuro_2011_talk.pdf | Penanen Lecture Slides]]

''Suggested Further Reading''
:*[http://www.ncbi.nlm.nih.gov/pubmed/18328753?dopt=Citation Parallel MRI at microtesla fields. Zotev VS, Volegov PL, Matlashov AN, Espy MA, Mosher JC, Kraus RH Jr. J Magn Reson. 2008 Jun;192(2):197-208. Epub 2008 Mar 6]

:*[http://www.ncbi.nlm.nih.gov/pubmed/17029228?dopt=Citation Three-dimensional prepolarized magnetic resonance imaging using rapid acquisition with relaxation enhancement. Matter NI, Scott GC, Venook RD, Ungersma SE, Grafendorfer T, Macovski A, Conolly SM. Magn Reson Med. 2006 Nov;56(5):1085-95.]

:*[http://iopscience.iop.org/0953-2048/19/5/S01/ How the SQUID was born. AH Silver. Superconductor Science and Technology Volume 19, Number 5, 2006]

:*John Clarke, SQUIDs: Scientific American, August 1994.

==''Friday 2/7/12'' - Positron Emission Tomography (PET). ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlbom]==
OUTLINE
[[image:ParallaxError.jpg|right]]
''Required Readings''
:*[[media:PET_2010.pdf | PET Imaging handout]]

''Suggested Further Reading''
:*READING

==''Wednesday 2/9/12'' - Transcranial Magneto Stimulation (TMS). ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]==

=Week 7 Spectroscopy and PET=
Both PET and MRI are means of localizing specific molecular species. MRI has lower sensitivity but good quantitative accuracy and the ability to simultaneously image and study multiple molecules and compounds. Our lecture on PET will consider the actual imaging device, its sensitivity and its limitations.
==''Friday 2/14/12'' - Magnetic Resonance Spectroscopy. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=45540 Jeffry Alger]==
OUTLINE
''Required Readings''
:*[[media:Alger MRS 20100512.pdf | Spectroscopy Lecture Slides]]

''Suggested Further Reading''
A question came up from the audience about the problem of simultaneously space and chemical shift by frequency. For an amusing story about the problem, you might want to read:

:*[http://muse.jhu.edu/journals/perspectives_on_science/v007/7.2baird02.html MS Cohen and D Baird, “Why Trade?: How zones of trade support epistemic stability.” Perspective on Science, 7(2): p. 231-254. 1999.]

=Week 8 Machine Learning=
This week we will look at modern and advanced analytic methods broadly called machine learning, or statistical pattern analysis. These methods are of great interest in the imaging community as they offer high sensitivity, the ability to explore activity at the systems level and the potential for ''predictive'' analysis and brain reading.
==''Friday 2/21/12'' - Presidents Day.==
''Suggested Further Reading''
:*[http://en.wikipedia.org/wiki/George_Washington George Washington]
:*[http://en.wikipedia.org/wiki/Abraham_Lincoln Abraham Lincoln]
==''Wednesday 2/23/12'' - PCA, ICA, Machine learning. ''Speaker'': [http://www.stat.ucla.edu/~yuille/index.html Alan Yuille]==
OUTLINE
[[image:Probmodel.jpg|right]]
''Required Readings''
:*READING

''Suggested Further Reading''
:*READING

=Week 9 Functional Connectivity, Multimodal Integration=
WEEKLYSUMMARY
==''Friday 2/28/12'' - Functional Connectivity. ''Speaker'': [http://alenarto.bol.ucla.edu/ Agatha Lenartowicz]==
OUTLINE

''Required Readings''
:*[[media:functionalconnectivity.pdf | Functional Connectivity Lecture Slides]]

''Suggested Further Reading''

Useful software for exploring functional connectivity (correlations/bivariate/partial etc) from Susan Whitfield-Gabrieli at MIT (link courtesy of Sam):*[http://web.mit.edu/swg/software.htm]

And additional readings in defense of DCM (other key papers are referenced in the slides)

Lee et al 2006 "Large-scale neural models and dynamic causal modelling"

David et al 2008 "Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation"

Schuyler et al 2010 "Dynamic Causal Modeling applied to fMRI data shows high reliability"

==''Wednesday 3/2/12'' - Multimodal Integration. ''Speaker'': [http://www.brainmapping.org/MarkCohen Cohen]==
OUTLINE
''Required Readings''
:*[[media:Multimodal_Imaging_2011.pdf | Lecture Slides for 3-2-11]]

=Week 10 tbd=
This week is presently left open for added topics and makeup as needed.
==''Friday 3/7/12'' - Final Distributed. ''MSC''==
OUTLINE
''Required Readings''
:*READING

''Suggested Further Reading''
:*READING

==''Wednesday 3/9/12'' - ''[mailto:stm@ucla.edu Paul Weiss] and [mailto:aandrews@mednet.ucla.edu Anne Andrews]'': [http://www.brainmapping.org/MarkCohen Cohen]==
Direct Nanoscale and Molecular Imaging.
''Required Readings''
:*[[media:AndrewsAM_Part1_09Mar2011.pdf | Andrews Lecture Slides]]
:*[[media:PWeissNITP2011.pdf‎ | Weiss Lecture Slides]]

''Suggested Further Reading''
:*READING

=Finals Week=

File:Compressed imaging tutorial.pdf

2012-03-07T22:16:13Z

Alhead: Compressed imaging tutorial by Dr. Kevin F. Kelly of Rice University. (2012)

Compressed imaging tutorial by Dr. Kevin F. Kelly of Rice University. (2012)

Principles of Neuroimaging A - 2010

2010-11-04T22:15:34Z

Alhead: /* MIDTERM POSTED */ Date was incorrectly listed as Wed. 11/8 instead of Mon.

Principles of Neuroimaging A, Fall, 2010 - Class Schedule and Syllabus

:'''[[Principles_of_Neuroimaging_-_2010-2011 | Back to main course page for Principles of Neuroimaging]]'''

:'''[[Principles_of_Neuroimaging_B_-_2011 | M284B Principles of Neuroimaging B]]'''

=Week 1: Orientation to Neuroimaging, Neurons, Brains=
==''Monday 9/27/10'' - Orientation & Neurons. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
In this first class we will review the basics of neurophysiology with an eye towards what signals of brain function might be visible to the neuroimager. We will discuss information coding, energetics, size and time scales.
[[Image:Neurons.jpg|right]]
''Required Readings''
:*[http://www.ccn.ucla.edu/wiki/images/8/81/The_Active_Brain.pdf The Active Brain]
:*[[media:NeuronFunction+AnatomyNITP.pdf‎| Neuron function slides shown in class]]
:*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]
''Suggested Further Reading''
:*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf "If Neuroimaging is the Answer, What is the Question?" Kosslyn, 1999]
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]
:*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., "Principles of Neural Science"]
:This paper, by Malhi, is a nice orientation in methods of neuroimaging. *[http://www.ccn.ucla.edu/wiki/images/f/f2/Malhi2007.pdf Making sense of neuroimaging in psychiatry]
:*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]

==''Wednesday 9/29/10'' - The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]==
'''A probe mail was sent this afternoon to all students in the class. If you did not receive this (subject, "A Probing Question"), let [mailto:mscohen@ucla.edu me] know'''

We will discuss the general organization of the human brain, and the regional specialization of cortical areas. The emphasis will be on understanding principles of organization:
*Phylogenetic Layering
*Functional Specialization
*Principles Divisions of the Brain
*Brain Systems

''Required Readings''
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[[media:NITPanatomy-Bookheimer.pdf | Slides shown in Class]]
''Suggested Further Reading''

[[media:PNIA2010-PS1.pdf|'''Problem Set 1 Neuroanatomy. Due in class 10/6.''']] Please remember that the preferred way for us to receive problem sets is ''via email'' to [mailto:mscohen@ucla.edu Mark] and to [mailto:alheadbme@ucla.edu Austin].
----
We will be studying linear systems next week. This coming week until Monday would be a good time to review your calculus fundamentals:
:''Derivatives of Polynomials''
:''Integrals of polynomials''
:''Basic trig + derivatives and integrals of sine and cosine functions''

When we start on the linear systems section, we will be using these fundamentals to develop the LaPlace and Fourier transforms, which involve the use of imaginary numbers. The math content for that section is largely contained in this link: [[Media: MathematicalTools.pdf | Mathematical Tools]].

Please let me know by email or other means if this material looks too difficult.

You will need to have matlab installed and running to do the next problem set.

=Week 2: Linear Systems=
Why the emphasis on Linear Systems? Because they are actually ''easy'' (as compared to non-linear systems, which are not.) As we go through this course, we will see many ways in which linear systems theory is applied to:
:Modeling of Neural Systems
:Extraction of Signal from Noise
:Design of Circuits
:Image Enhancement
:Understanding of Image artifacts, and others.

Linear systems analysis is one of the great technologies of the 20th and 21st century. It is now the basis for virtually all electronics design, and its extension into the discrete (digital) domain is the basis for most of modern signal processing.

In our specific case, we will use these few basic principles of linear systems to understand both the instruments we use and the neuroimaging signals we collect. When you have mastered this material, you should be in a much better position to model the systems that you study in order to develop an approach to studying them.

Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer on imaginary numbers] that might be a helpful review.

==''Monday 10/4/10'' - Transforms and the Convolution Theorem. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==

''Required Readings''
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1
:*[[Media: Mathematical_tools.pdf|Mathematical Tools]] - updated 10/4/10 after class

''Suggested Further Reading''
:'''Problem Set 2A - Introduction to matlab'''

''Slides shown in class''
:[[media:LinearityM285.pdf|Linearity and the Fourier Transform]] - updated 10/4/10 after class

Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]

If you are the type who sees beauty in mathematics, the Euler identity may be one of the most beautiful pieces of math in the world.

==''Wednesday 10/6/10'' - Fourier Transform Properties. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
[[Image:xkcd_fourier.jpg|right]]
*Example transform derivations
*The Convolution theorem
*Oddness (and Even-ness)
*The Fourier Shift Theorem
Please see [http://www.brainmapping.org/NITP/PNA/html/ShowConvolutions.html MATLAB demo of Fourier transforms and convolution]

Optional Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 5 through 9
**Note: This reading may be heavy going. I will not be going into nearly this much detail in class, but your time on this will be very well spent. We will be revisiting this material later in the course in week 5.

'''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''
:*[http://www.dspguide.com/CH5.PDF Linear Systems]
:*[http://www.dspguide.com/CH6.PDF Convolution]
:*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]
:''Note: These chapters are lite on math and try to focus on a conceptual understanding''

:'''Problem Set 2B modeling in matlab'''

[[Media: ProblemSet3A.pdf|Problem Set 2A]] and
[http://www.brainmapping.org/NITP/PNA/html/TwoDimensions.html Problem Set 2B]

----
Practice using the Fourier transform:
:[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').]
:[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]
----

I suggest very strongly that you brush up on linear algebra during this week in anticipation of Dr. Sugar's lectures in statistics. In particular, I would like you to have an understanding of :

:''Matrices as solutions to linear equations - determinants and inverses''
:''Matrix multiplication''

For these, I can recommend the Hefferon text noted above.

=Week 3: Noise and Basic Statistics=
==''Monday 10/11/10'' - Noise. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
It is what you ''don't'' want.
:Additive noise
:White Noise
:Boltzmann noise
:Colored Noise
:Gaussian Noise
:Coherent noise
:Sampling Errors
:Aliasing
:Quantization noise
:Spectral filtering

Noise comes in all shapes and colors. It is present in every measurement we make, from an EEG voltage to an estimate of the effects of dopamine on forebrain signal. Our best weapons are an understanding of the statistical properties of noise, the sources of noise and the ways to control it. Noise in the discrete digital domain is special, as it is both ''created'' by digitization and amplified by sampling.

Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4

:*Slides used in Class:
[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]
:'''Problem set 3 - properties of noise'''

==''Wednesday 10/13/10'' - Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.
[[Image:MeasureForMeasure.jpg|right]]

:*[[media: CohenClassIntroStats10_13_10.pdf | Slides used in class (set 1)]]

''Review of'':
:*Descriptive Statistics: mean, mode, variance, standard deviation
:*Statistical Inference. The Binomial and Normal Distribution
:*Basic Tests: t-test, linear correlation
:*Modeling and non-linear relations
:*Bayes rule

Suggested reading
:*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]
:*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]
:The latter teaches stats at what I feel to be the right level - developing intuitions about the kinds of questions that can be answered using stats and about the statistical tests and measures

:'''Problem Set 5 - Statistics in matlab'''
::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]
::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]

=Week4: Statistics for Imaging=
==''Monday 10/18/10'' - Statistics for Imaging I. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
#Outline
[[image:BVTradeoff.jpg|right]]
''Required Readings''
:*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]
:*[[media: CohenClassSlides10_18_10.pdf | Slides used in class (set 2)]]

:*The General Linear Model
*Linear Algebra applied to Statistical Solutions
:*Analysis of Variance

''Suggested Further Reading''

==''Wednesday 10/20/10'' - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
*Fixed and Random Effects
*Repeated measures
:*Bonferroni and Other Corrections
*Non-Parametric Methods
*Autocorrelation
*Unknown Distributions

''Required Readings''
:*[[media: CohenClassSlides10_20_10.pdf | Slides used in class (set 3)]]

''Suggested Further Reading''

=Week 5: Optics=
The prototypical imaging means: Direct visualization. These lectures will cover the principles of light transmission, refraction, reflection and dispersion and will develop a quantitative approach to the analysis of optical systems. We will cover the theory of lenses, imperfections in focus, such as chromatic aberration, and a model of optical devices that builds on our understanding of convolution.
==''Monday 10/25/10'' - Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==
[[Image:Reflection.jpg|right]]
The overall goal of this lecture is to establish that:
''- Physical constants have tangible meanings''
''- Plane waves form a physically unrealizable but extremely good approximation to real systems''
''- Boundaries bend light''
''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''
''- The PSF gives a good indication of the overall performance of an imaging system''
''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''

'''Outline:'''
:* Constitutive parameters (ε, μ, η, n, etc.)
:* Plane wave basics
:* Plane waves at boundaries
:* Lenses
:* Advanced imaging properties of lenses
:* Point spread function.

''Required Readings''
Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].
''Suggested Further Reading''

==''Wednesday 10/27/10'' - Optics II. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==

''Required Readings''

''Suggested Further Reading''

=Week 6: Optical Neuroimaging=
== MIDTERM POSTED ==
:Click [[media:MidTermFall2010.pdf‎ | here for the Midterm. Due in class Mon. 11/8]]

==''Monday 11/1/10'' - Optical Applications. ''Speaker'': tbd==

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/3/10'' - Optical and flourescence methods in dynamic neural systems. ''Speaker'': [mailto:kmcevoy@ucla.edu Kevin McEvoy]==
#Outline
''Required Readings''
:*[http://ccn.ucla.edu/wiki/images/d/d3/NeuroimagingCellularLevel_KMcEvoy_2010.pdf Lecture Slides]

=Week 7: Optical Intrinsic Imaging, Beginning Circuits=
==''Monday 11/8/10'' - Wide field Optical imaging. ''Speaker'': [http://www.uclahealth.org/body.cfm?xyzpdqabc=0&id=479&action=detail&ref=95328 Nader Pouratian]==

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/10/10'' - Circuits I. [http://www.brainmapping.org/MarkCohen Mark Cohen]==
Why circuits?
:(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly
:The device you ''really'' want in your lab doesn't exist. You very well may have to make it.
:There are electronic analogs to most of the linear systems that you have so far studied (and ''vice versa'' - the tools you now understand can be used to analyze and predict circuit behavior).

If you have not had any of this background, you might want to have a look at this handout, [[Media:Electricity.pdf|Electrical Circuits]], in advance. There are near infinite numbers of resources on the web that cover similar material (near enough to infinite that by the time you read all of them, there would be a whole new set.) I have recently come across a link to [http://www.allaboutcircuits.com/ Online Books: All About Circuits] ''IF'' you want practical hands-on knowledge about this material, my all-time favorite text is [http://www.google.com/products/catalog?hl=en&client=safari&rls=en-us&ei=uVSPSfaxE5nMsAPf-tmSCQ&resnum=1&q=art+of+electronics&um=1&ie=UTF-8&cid=8820839049329255765#ps-sellers "Horowitz and Hill: ''The Art of Electronics.''"] The latest edition, however, is dated 1989 and a new third edition is promised. I have therefore stopped short of recommending a purchase unless your need to make circuits is immediate. In this book, you will find an excellent education on the fundamental principles of electrical circuits and an incredible compendium of practical data, such as how to assemble circuit boards, how to make measurements, etc...)

I found a nice [http://video.google.com/videoplay?docid=5645396659673218353&q=Physics+for+Future+Presidents+Electricity&total=5&start=0&num=10&so=0&type=search&plindex=0#0h20m30s intro lecture on charge, current and voltage].

Readings:
:*[[Media: Circuits.pdf|Circuits 1 & 2]]
:*[http://www.brainmapping.org/NITP/PNA/Readings/Circuits.pdf Slides shown in class (''revised 10:30pm 1/28/2010'')]
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10
**You may or may not find this comprehensible without chapters 5 through 9.

We will discuss:
:*Passive Circuit Elements: Resistors, Capacitors, Inductors
:*Gain
:*Transformers
:*Rectifiers
:*Active Elements
::- ''Amplifiers''
::- ''Transistors''
::- ''Op Amps''
:*Solutions with Matrices
''Suggested Further Reading''

=Week 8: Electricity and Electronics. Human Electrophysiology=
==''Monday 11/15/10'' - Electricity and Electronics. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
[[Image:Opamp.jpg|right]]
*Laplace transform analysis
*Op Amp Circuits
*Active Filters
*Noise Control

''Required Readings''

''Suggested Further Reading''
Please note that I have the components we used for the class demos available for you to play with at your leisure.

==''Wednesday 11/17/10'' - Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]==
''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]
*A look at real EEG data
*Preprocessing:
**filtering
**artifact detection/removal
*averaging
*single events
*interpretation

''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]
*Normal and Abnormal EEG
*EEG as a marker for brain state
**sleep staging
**alpha and relaxation
*Neurofeedback???

=Week 9: Practical Electronic Circuits=
This week we will design, build and test a practical device for recording of human electrical potentials: The electromyogram, or EMG. This device must manage the many challenges of interfacing with small biological signals: Sensitivity, Gain, Noise, Linearity, Filtering. The recording we (''hopefully'') will make will demonstrate issues of linearity and neural coding.

==''Monday 11/22/10'' - Design of an EMG Preamp. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
#Outline

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/24/10'' - Building and Using Electronic Devices: ''EMG''. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
#Outline

''Required Readings''

''Suggested Further Reading''

=Week 10: Filters=
==''Monday 12/1/10'' - Autocorrelation, Filters and Color. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==

''Required Readings''
Most of what we will look at today is in chapter 7 & 8 of Van Drongelen.

''Suggested Further Reading''

==''Wednesday 12/3/10'' - '''Finals Begin'''

Principles of Neuroimaging A - 2010

2010-10-21T19:32:47Z

Alhead: /* ''Wednesday 10/20/10'' - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar] */ Added slides

Principles of Neuroimaging A, Fall, 2010 - Class Schedule and Syllabus

:'''[[Principles_of_Neuroimaging_-_2010-2011 | Back to main course page for Principles of Neuroimaging]]'''

:'''[[Principles_of_Neuroimaging_B_-_2011 | M284B Principles of Neuroimaging B]]'''

=Week 1: Orientation to Neuroimaging, Neurons, Brains=
==''Monday 9/27/10'' - Orientation & Neurons. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
In this first class we will review the basics of neurophysiology with an eye towards what signals of brain function might be visible to the neuroimager. We will discuss information coding, energetics, size and time scales.
[[Image:Neurons.jpg|right]]
''Required Readings''
:*[http://www.ccn.ucla.edu/wiki/images/8/81/The_Active_Brain.pdf The Active Brain]
:*[[media:NeuronFunction+AnatomyNITP.pdf‎| Neuron function slides shown in class]]
:*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]
''Suggested Further Reading''
:*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf "If Neuroimaging is the Answer, What is the Question?" Kosslyn, 1999]
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]
:*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., "Principles of Neural Science"]
:This paper, by Malhi, is a nice orientation in methods of neuroimaging. *[http://www.ccn.ucla.edu/wiki/images/f/f2/Malhi2007.pdf Making sense of neuroimaging in psychiatry]
:*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]

==''Wednesday 9/29/10'' - The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]==
'''A probe mail was sent this afternoon to all students in the class. If you did not receive this (subject, "A Probing Question"), let [mailto:mscohen@ucla.edu me] know'''

We will discuss the general organization of the human brain, and the regional specialization of cortical areas. The emphasis will be on understanding principles of organization:
*Phylogenetic Layering
*Functional Specialization
*Principles Divisions of the Brain
*Brain Systems

''Required Readings''
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[[media:NITPanatomy-Bookheimer.pdf | Slides shown in Class]]
''Suggested Further Reading''

[[media:PNIA2010-PS1.pdf|'''Problem Set 1 Neuroanatomy. Due in class 10/6.''']] Please remember that the preferred way for us to receive problem sets is ''via email'' to [mailto:mscohen@ucla.edu Mark] and to [mailto:alheadbme@ucla.edu Austin].
----
We will be studying linear systems next week. This coming week until Monday would be a good time to review your calculus fundamentals:
:''Derivatives of Polynomials''
:''Integrals of polynomials''
:''Basic trig + derivatives and integrals of sine and cosine functions''

When we start on the linear systems section, we will be using these fundamentals to develop the LaPlace and Fourier transforms, which involve the use of imaginary numbers. The math content for that section is largely contained in this link: [[Media: MathematicalTools.pdf | Mathematical Tools]].

Please let me know by email or other means if this material looks too difficult.

You will need to have matlab installed and running to do the next problem set.

=Week 2: Linear Systems=
Why the emphasis on Linear Systems? Because they are actually ''easy'' (as compared to non-linear systems, which are not.) As we go through this course, we will see many ways in which linear systems theory is applied to:
:Modeling of Neural Systems
:Extraction of Signal from Noise
:Design of Circuits
:Image Enhancement
:Understanding of Image artifacts, and others.

Linear systems analysis is one of the great technologies of the 20th and 21st century. It is now the basis for virtually all electronics design, and its extension into the discrete (digital) domain is the basis for most of modern signal processing.

In our specific case, we will use these few basic principles of linear systems to understand both the instruments we use and the neuroimaging signals we collect. When you have mastered this material, you should be in a much better position to model the systems that you study in order to develop an approach to studying them.

Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer on imaginary numbers] that might be a helpful review.

==''Monday 10/4/10'' - Transforms and the Convolution Theorem. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==

''Required Readings''
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1
:*[[Media: Mathematical_tools.pdf|Mathematical Tools]] - updated 10/4/10 after class

''Suggested Further Reading''
:'''Problem Set 2A - Introduction to matlab'''

''Slides shown in class''
:[[media:LinearityM285.pdf|Linearity and the Fourier Transform]] - updated 10/4/10 after class

Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]

If you are the type who sees beauty in mathematics, the Euler identity may be one of the most beautiful pieces of math in the world.

==''Wednesday 10/6/10'' - Fourier Transform Properties. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
[[Image:xkcd_fourier.jpg|right]]
*Example transform derivations
*The Convolution theorem
*Oddness (and Even-ness)
*The Fourier Shift Theorem
Please see [http://www.brainmapping.org/NITP/PNA/html/ShowConvolutions.html MATLAB demo of Fourier transforms and convolution]

Optional Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 5 through 9
**Note: This reading may be heavy going. I will not be going into nearly this much detail in class, but your time on this will be very well spent. We will be revisiting this material later in the course in week 5.

'''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''
:*[http://www.dspguide.com/CH5.PDF Linear Systems]
:*[http://www.dspguide.com/CH6.PDF Convolution]
:*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]
:''Note: These chapters are lite on math and try to focus on a conceptual understanding''

:'''Problem Set 2B modeling in matlab'''

[[Media: ProblemSet3A.pdf|Problem Set 2A]] and
[http://www.brainmapping.org/NITP/PNA/html/TwoDimensions.html Problem Set 2B]

----

I suggest very strongly that you brush up on linear algebra during this week in anticipation of Dr. Sugar's lectures in statistics. In particular, I would like you to have an understanding of :

:''Matrices as solutions to linear equations - determinants and inverses''
:''Matrix multiplication''

For these, I can recommend the Hefferon text noted above.

=Week 3: Noise and Basic Statistics=
==''Monday 10/11/10'' - Noise. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
It is what you ''don't'' want.
:Additive noise
:White Noise
:Boltzmann noise
:Colored Noise
:Gaussian Noise
:Coherent noise
:Sampling Errors
:Aliasing
:Quantization noise
:Spectral filtering

Noise comes in all shapes and colors. It is present in every measurement we make, from an EEG voltage to an estimate of the effects of dopamine on forebrain signal. Our best weapons are an understanding of the statistical properties of noise, the sources of noise and the ways to control it. Noise in the discrete digital domain is special, as it is both ''created'' by digitization and amplified by sampling.

Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4

:*Slides used in Class:
[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]
:'''Problem set 3 - properties of noise'''

==''Wednesday 10/13/10'' - Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.
[[Image:MeasureForMeasure.jpg|right]]

:*[[media: CohenClassIntroStats10_13_10.pdf | Slides used in class (set 1)]]

''Review of'':
:*Descriptive Statistics: mean, mode, variance, standard deviation
:*Statistical Inference. The Binomial and Normal Distribution
:*Basic Tests: t-test, linear correlation
:*Modeling and non-linear relations
:*Bayes rule

Suggested reading
:*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]
:*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]
:The latter teaches stats at what I feel to be the right level - developing intuitions about the kinds of questions that can be answered using stats and about the statistical tests and measures

:'''Problem Set 5 - Statistics in matlab'''
::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]
::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]

=Week4: Statistics for Imaging=
==''Monday 10/18/10'' - Statistics for Imaging I. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
#Outline
[[image:BVTradeoff.jpg|right]]
''Required Readings''
:*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]
:*[[media: CohenClassSlides10_18_10.pdf | Slides used in class (set 2)]]

:*The General Linear Model
*Linear Algebra applied to Statistical Solutions
:*Analysis of Variance

''Suggested Further Reading''

==''Wednesday 10/20/10'' - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
*Fixed and Random Effects
*Repeated measures
:*Bonferroni and Other Corrections
*Non-Parametric Methods
*Autocorrelation
*Unknown Distributions

''Required Readings''
:*[[media: CohenClassSlides10_20_10.pdf | Slides used in class (set 3)]]

''Suggested Further Reading''

=Week 5: Optics=
The prototypical imaging means: Direct visualization. These lectures will cover the principles of light transmission, refraction, reflection and dispersion and will develop a quantitative approach to the analysis of optical systems. We will cover the theory of lenses, imperfections in focus, such as chromatic aberration, and a model of optical devices that builds on our understanding of convolution.
==''Monday 10/25/10'' - Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==
[[Image:Reflection.jpg|right]]
The overall goal of this lecture is to establish that:
''- Physical constants have tangible meanings''
''- Plane waves form a physically unrealizable but extremely good approximation to real systems''
''- Boundaries bend light''
''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''
''- The PSF gives a good indication of the overall performance of an imaging system''
''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''

'''Outline:'''
:* Constitutive parameters (ε, μ, η, n, etc.)
:* Plane wave basics
:* Plane waves at boundaries
:* Lenses
:* Advanced imaging properties of lenses
:* Point spread function.

''Required Readings''
Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].
''Suggested Further Reading''

==''Wednesday 10/27/10'' - Optics II. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==

''Required Readings''

''Suggested Further Reading''

=Week 6: Optical Neuroimaging=
==''Monday 11/1/10'' - Optical Applications. ''Speaker'': tbd==

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/3/10'' - Optical and flourescence methods in dynamic neural systems. ''Speaker'': [mailto:kmcevoy@ucla.edu Kevin McEvoy]==
#Outline
''Required Readings''
:*[http://ccn.ucla.edu/wiki/images/d/d3/NeuroimagingCellularLevel_KMcEvoy_2010.pdf Lecture Slides]

=Week 7: Optical Intrinsic Imaging, Beginning Circuits=
==''Monday 11/8/10'' - Wide field Optical imaging. ''Speaker'': [http://www.uclahealth.org/body.cfm?xyzpdqabc=0&id=479&action=detail&ref=95328 Nader Pouratian]==

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/10/10'' - Circuits I. [http://www.brainmapping.org/MarkCohen Mark Cohen]==
Why circuits?
:(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly
:The device you ''really'' want in your lab doesn't exist. You very well may have to make it.
:There are electronic analogs to most of the linear systems that you have so far studied (and ''vice versa'' - the tools you now understand can be used to analyze and predict circuit behavior).

If you have not had any of this background, you might want to have a look at this handout, [[Media:Electricity.pdf|Electrical Circuits]], in advance. There are near infinite numbers of resources on the web that cover similar material (near enough to infinite that by the time you read all of them, there would be a whole new set.) I have recently come across a link to [http://www.allaboutcircuits.com/ Online Books: All About Circuits] ''IF'' you want practical hands-on knowledge about this material, my all-time favorite text is [http://www.google.com/products/catalog?hl=en&client=safari&rls=en-us&ei=uVSPSfaxE5nMsAPf-tmSCQ&resnum=1&q=art+of+electronics&um=1&ie=UTF-8&cid=8820839049329255765#ps-sellers "Horowitz and Hill: ''The Art of Electronics.''"] The latest edition, however, is dated 1989 and a new third edition is promised. I have therefore stopped short of recommending a purchase unless your need to make circuits is immediate. In this book, you will find an excellent education on the fundamental principles of electrical circuits and an incredible compendium of practical data, such as how to assemble circuit boards, how to make measurements, etc...)

I found a nice [http://video.google.com/videoplay?docid=5645396659673218353&q=Physics+for+Future+Presidents+Electricity&total=5&start=0&num=10&so=0&type=search&plindex=0#0h20m30s intro lecture on charge, current and voltage].

Readings:
:*[[Media: Circuits.pdf|Circuits 1 & 2]]
:*[http://www.brainmapping.org/NITP/PNA/Readings/Circuits.pdf Slides shown in class (''revised 10:30pm 1/28/2010'')]
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10
**You may or may not find this comprehensible without chapters 5 through 9.

We will discuss:
:*Passive Circuit Elements: Resistors, Capacitors, Inductors
:*Gain
:*Transformers
:*Rectifiers
:*Active Elements
::- ''Amplifiers''
::- ''Transistors''
::- ''Op Amps''
:*Solutions with Matrices
''Suggested Further Reading''

=Week 8: Electricity and Electronics. Human Electrophysiology=
==''Monday 11/15/10'' - Electricity and Electronics. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
[[Image:Opamp.jpg|right]]
*Laplace transform analysis
*Op Amp Circuits
*Active Filters
*Noise Control

''Required Readings''

''Suggested Further Reading''
Please note that I have the components we used for the class demos available for you to play with at your leisure.

==''Wednesday 11/17/10'' - Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]==
''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]
*A look at real EEG data
*Preprocessing:
**filtering
**artifact detection/removal
*averaging
*single events
*interpretation

''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]
*Normal and Abnormal EEG
*EEG as a marker for brain state
**sleep staging
**alpha and relaxation
*Neurofeedback???

=Week 9: Practical Electronic Circuits=
This week we will design, build and test a practical device for recording of human electrical potentials: The electromyogram, or EMG. This device must manage the many challenges of interfacing with small biological signals: Sensitivity, Gain, Noise, Linearity, Filtering. The recording we (''hopefully'') will make will demonstrate issues of linearity and neural coding.

==''Monday 11/22/10'' - Design of an EMG Preamp. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
#Outline

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/24/10'' - Building and Using Electronic Devices: ''EMG''. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
#Outline

''Required Readings''

''Suggested Further Reading''

=Week 10: Filters=
==''Monday 12/1/10'' - Autocorrelation, Filters and Color. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==

''Required Readings''
Most of what we will look at today is in chapter 7 & 8 of Van Drongelen.

''Suggested Further Reading''

==''Wednesday 12/3/10'' - '''Finals Begin'''

File:CohenClassSlides10 20 10.pdf

2010-10-21T19:31:45Z

Alhead: Third set of slides from Dr. Catherine Sugar's lectures.

Third set of slides from Dr. Catherine Sugar's lectures.

Principles of Neuroimaging A - 2010

2010-10-21T19:31:07Z

Alhead: /* ''Monday 10/18/10'' - Statistics for Imaging I. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar] */ Added slides

Principles of Neuroimaging A, Fall, 2010 - Class Schedule and Syllabus

:'''[[Principles_of_Neuroimaging_-_2010-2011 | Back to main course page for Principles of Neuroimaging]]'''

:'''[[Principles_of_Neuroimaging_B_-_2011 | M284B Principles of Neuroimaging B]]'''

=Week 1: Orientation to Neuroimaging, Neurons, Brains=
==''Monday 9/27/10'' - Orientation & Neurons. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
In this first class we will review the basics of neurophysiology with an eye towards what signals of brain function might be visible to the neuroimager. We will discuss information coding, energetics, size and time scales.
[[Image:Neurons.jpg|right]]
''Required Readings''
:*[http://www.ccn.ucla.edu/wiki/images/8/81/The_Active_Brain.pdf The Active Brain]
:*[[media:NeuronFunction+AnatomyNITP.pdf‎| Neuron function slides shown in class]]
:*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]
''Suggested Further Reading''
:*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf "If Neuroimaging is the Answer, What is the Question?" Kosslyn, 1999]
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]
:*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., "Principles of Neural Science"]
:This paper, by Malhi, is a nice orientation in methods of neuroimaging. *[http://www.ccn.ucla.edu/wiki/images/f/f2/Malhi2007.pdf Making sense of neuroimaging in psychiatry]
:*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]

==''Wednesday 9/29/10'' - The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]==
'''A probe mail was sent this afternoon to all students in the class. If you did not receive this (subject, "A Probing Question"), let [mailto:mscohen@ucla.edu me] know'''

We will discuss the general organization of the human brain, and the regional specialization of cortical areas. The emphasis will be on understanding principles of organization:
*Phylogenetic Layering
*Functional Specialization
*Principles Divisions of the Brain
*Brain Systems

''Required Readings''
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[[media:NITPanatomy-Bookheimer.pdf | Slides shown in Class]]
''Suggested Further Reading''

[[media:PNIA2010-PS1.pdf|'''Problem Set 1 Neuroanatomy. Due in class 10/6.''']] Please remember that the preferred way for us to receive problem sets is ''via email'' to [mailto:mscohen@ucla.edu Mark] and to [mailto:alheadbme@ucla.edu Austin].
----
We will be studying linear systems next week. This coming week until Monday would be a good time to review your calculus fundamentals:
:''Derivatives of Polynomials''
:''Integrals of polynomials''
:''Basic trig + derivatives and integrals of sine and cosine functions''

When we start on the linear systems section, we will be using these fundamentals to develop the LaPlace and Fourier transforms, which involve the use of imaginary numbers. The math content for that section is largely contained in this link: [[Media: MathematicalTools.pdf | Mathematical Tools]].

Please let me know by email or other means if this material looks too difficult.

You will need to have matlab installed and running to do the next problem set.

=Week 2: Linear Systems=
Why the emphasis on Linear Systems? Because they are actually ''easy'' (as compared to non-linear systems, which are not.) As we go through this course, we will see many ways in which linear systems theory is applied to:
:Modeling of Neural Systems
:Extraction of Signal from Noise
:Design of Circuits
:Image Enhancement
:Understanding of Image artifacts, and others.

Linear systems analysis is one of the great technologies of the 20th and 21st century. It is now the basis for virtually all electronics design, and its extension into the discrete (digital) domain is the basis for most of modern signal processing.

In our specific case, we will use these few basic principles of linear systems to understand both the instruments we use and the neuroimaging signals we collect. When you have mastered this material, you should be in a much better position to model the systems that you study in order to develop an approach to studying them.

Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer on imaginary numbers] that might be a helpful review.

==''Monday 10/4/10'' - Transforms and the Convolution Theorem. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==

''Required Readings''
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1
:*[[Media: Mathematical_tools.pdf|Mathematical Tools]] - updated 10/4/10 after class

''Suggested Further Reading''
:'''Problem Set 2A - Introduction to matlab'''

''Slides shown in class''
:[[media:LinearityM285.pdf|Linearity and the Fourier Transform]] - updated 10/4/10 after class

Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]

If you are the type who sees beauty in mathematics, the Euler identity may be one of the most beautiful pieces of math in the world.

==''Wednesday 10/6/10'' - Fourier Transform Properties. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
[[Image:xkcd_fourier.jpg|right]]
*Example transform derivations
*The Convolution theorem
*Oddness (and Even-ness)
*The Fourier Shift Theorem
Please see [http://www.brainmapping.org/NITP/PNA/html/ShowConvolutions.html MATLAB demo of Fourier transforms and convolution]

Optional Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 5 through 9
**Note: This reading may be heavy going. I will not be going into nearly this much detail in class, but your time on this will be very well spent. We will be revisiting this material later in the course in week 5.

'''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''
:*[http://www.dspguide.com/CH5.PDF Linear Systems]
:*[http://www.dspguide.com/CH6.PDF Convolution]
:*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]
:''Note: These chapters are lite on math and try to focus on a conceptual understanding''

:'''Problem Set 2B modeling in matlab'''

[[Media: ProblemSet3A.pdf|Problem Set 2A]] and
[http://www.brainmapping.org/NITP/PNA/html/TwoDimensions.html Problem Set 2B]

----

I suggest very strongly that you brush up on linear algebra during this week in anticipation of Dr. Sugar's lectures in statistics. In particular, I would like you to have an understanding of :

:''Matrices as solutions to linear equations - determinants and inverses''
:''Matrix multiplication''

For these, I can recommend the Hefferon text noted above.

=Week 3: Noise and Basic Statistics=
==''Monday 10/11/10'' - Noise. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
It is what you ''don't'' want.
:Additive noise
:White Noise
:Boltzmann noise
:Colored Noise
:Gaussian Noise
:Coherent noise
:Sampling Errors
:Aliasing
:Quantization noise
:Spectral filtering

Noise comes in all shapes and colors. It is present in every measurement we make, from an EEG voltage to an estimate of the effects of dopamine on forebrain signal. Our best weapons are an understanding of the statistical properties of noise, the sources of noise and the ways to control it. Noise in the discrete digital domain is special, as it is both ''created'' by digitization and amplified by sampling.

Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4

:*Slides used in Class:
[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]
:'''Problem set 3 - properties of noise'''

==''Wednesday 10/13/10'' - Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.
[[Image:MeasureForMeasure.jpg|right]]

:*[[media: CohenClassIntroStats10_13_10.pdf | Slides used in class (set 1)]]

''Review of'':
:*Descriptive Statistics: mean, mode, variance, standard deviation
:*Statistical Inference. The Binomial and Normal Distribution
:*Basic Tests: t-test, linear correlation
:*Modeling and non-linear relations
:*Bayes rule

Suggested reading
:*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]
:*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]
:The latter teaches stats at what I feel to be the right level - developing intuitions about the kinds of questions that can be answered using stats and about the statistical tests and measures

:'''Problem Set 5 - Statistics in matlab'''
::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]
::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]

=Week4: Statistics for Imaging=
==''Monday 10/18/10'' - Statistics for Imaging I. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
#Outline
[[image:BVTradeoff.jpg|right]]
''Required Readings''
:*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]
:*[[media: CohenClassSlides10_18_10.pdf | Slides used in class (set 2)]]

:*The General Linear Model
*Linear Algebra applied to Statistical Solutions
:*Analysis of Variance

''Suggested Further Reading''

==''Wednesday 10/20/10'' - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
*Fixed and Random Effects
*Repeated measures
:*Bonferroni and Other Corrections
*Non-Parametric Methods
*Autocorrelation
*Unknown Distributions

''Required Readings''

''Suggested Further Reading''

=Week 5: Optics=
The prototypical imaging means: Direct visualization. These lectures will cover the principles of light transmission, refraction, reflection and dispersion and will develop a quantitative approach to the analysis of optical systems. We will cover the theory of lenses, imperfections in focus, such as chromatic aberration, and a model of optical devices that builds on our understanding of convolution.
==''Monday 10/25/10'' - Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==
[[Image:Reflection.jpg|right]]
The overall goal of this lecture is to establish that:
''- Physical constants have tangible meanings''
''- Plane waves form a physically unrealizable but extremely good approximation to real systems''
''- Boundaries bend light''
''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''
''- The PSF gives a good indication of the overall performance of an imaging system''
''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''

'''Outline:'''
:* Constitutive parameters (ε, μ, η, n, etc.)
:* Plane wave basics
:* Plane waves at boundaries
:* Lenses
:* Advanced imaging properties of lenses
:* Point spread function.

''Required Readings''
Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].
''Suggested Further Reading''

==''Wednesday 10/27/10'' - Optics II. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==

''Required Readings''

''Suggested Further Reading''

=Week 6: Optical Neuroimaging=
==''Monday 11/1/10'' - Optical Applications. ''Speaker'': tbd==

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/3/10'' - Optical and flourescence methods in dynamic neural systems. ''Speaker'': [mailto:kmcevoy@ucla.edu Kevin McEvoy]==
#Outline
''Required Readings''
:*[http://ccn.ucla.edu/wiki/images/d/d3/NeuroimagingCellularLevel_KMcEvoy_2010.pdf Lecture Slides]

=Week 7: Optical Intrinsic Imaging, Beginning Circuits=
==''Monday 11/8/10'' - Wide field Optical imaging. ''Speaker'': [http://www.uclahealth.org/body.cfm?xyzpdqabc=0&id=479&action=detail&ref=95328 Nader Pouratian]==

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/10/10'' - Circuits I. [http://www.brainmapping.org/MarkCohen Mark Cohen]==
Why circuits?
:(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly
:The device you ''really'' want in your lab doesn't exist. You very well may have to make it.
:There are electronic analogs to most of the linear systems that you have so far studied (and ''vice versa'' - the tools you now understand can be used to analyze and predict circuit behavior).

If you have not had any of this background, you might want to have a look at this handout, [[Media:Electricity.pdf|Electrical Circuits]], in advance. There are near infinite numbers of resources on the web that cover similar material (near enough to infinite that by the time you read all of them, there would be a whole new set.) I have recently come across a link to [http://www.allaboutcircuits.com/ Online Books: All About Circuits] ''IF'' you want practical hands-on knowledge about this material, my all-time favorite text is [http://www.google.com/products/catalog?hl=en&client=safari&rls=en-us&ei=uVSPSfaxE5nMsAPf-tmSCQ&resnum=1&q=art+of+electronics&um=1&ie=UTF-8&cid=8820839049329255765#ps-sellers "Horowitz and Hill: ''The Art of Electronics.''"] The latest edition, however, is dated 1989 and a new third edition is promised. I have therefore stopped short of recommending a purchase unless your need to make circuits is immediate. In this book, you will find an excellent education on the fundamental principles of electrical circuits and an incredible compendium of practical data, such as how to assemble circuit boards, how to make measurements, etc...)

I found a nice [http://video.google.com/videoplay?docid=5645396659673218353&q=Physics+for+Future+Presidents+Electricity&total=5&start=0&num=10&so=0&type=search&plindex=0#0h20m30s intro lecture on charge, current and voltage].

Readings:
:*[[Media: Circuits.pdf|Circuits 1 & 2]]
:*[http://www.brainmapping.org/NITP/PNA/Readings/Circuits.pdf Slides shown in class (''revised 10:30pm 1/28/2010'')]
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10
**You may or may not find this comprehensible without chapters 5 through 9.

We will discuss:
:*Passive Circuit Elements: Resistors, Capacitors, Inductors
:*Gain
:*Transformers
:*Rectifiers
:*Active Elements
::- ''Amplifiers''
::- ''Transistors''
::- ''Op Amps''
:*Solutions with Matrices
''Suggested Further Reading''

=Week 8: Electricity and Electronics. Human Electrophysiology=
==''Monday 11/15/10'' - Electricity and Electronics. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
[[Image:Opamp.jpg|right]]
*Laplace transform analysis
*Op Amp Circuits
*Active Filters
*Noise Control

''Required Readings''

''Suggested Further Reading''
Please note that I have the components we used for the class demos available for you to play with at your leisure.

==''Wednesday 11/17/10'' - Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]==
''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]
*A look at real EEG data
*Preprocessing:
**filtering
**artifact detection/removal
*averaging
*single events
*interpretation

''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]
*Normal and Abnormal EEG
*EEG as a marker for brain state
**sleep staging
**alpha and relaxation
*Neurofeedback???

=Week 9: Practical Electronic Circuits=
This week we will design, build and test a practical device for recording of human electrical potentials: The electromyogram, or EMG. This device must manage the many challenges of interfacing with small biological signals: Sensitivity, Gain, Noise, Linearity, Filtering. The recording we (''hopefully'') will make will demonstrate issues of linearity and neural coding.

==''Monday 11/22/10'' - Design of an EMG Preamp. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
#Outline

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/24/10'' - Building and Using Electronic Devices: ''EMG''. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
#Outline

''Required Readings''

''Suggested Further Reading''

=Week 10: Filters=
==''Monday 12/1/10'' - Autocorrelation, Filters and Color. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==

''Required Readings''
Most of what we will look at today is in chapter 7 & 8 of Van Drongelen.

''Suggested Further Reading''

==''Wednesday 12/3/10'' - '''Finals Begin'''

File:CohenClassSlides10 18 10.pdf

2010-10-21T19:29:06Z

Alhead:

Second set of slides from Dr. Catherine Sugar's lectures.

Principles of Neuroimaging A - 2010

2010-10-21T19:27:13Z

Alhead: /* ''Wednesday 10/13/10'' - Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar] */ Added slides

Principles of Neuroimaging A, Fall, 2010 - Class Schedule and Syllabus

:'''[[Principles_of_Neuroimaging_-_2010-2011 | Back to main course page for Principles of Neuroimaging]]'''

:'''[[Principles_of_Neuroimaging_B_-_2011 | M284B Principles of Neuroimaging B]]'''

=Week 1: Orientation to Neuroimaging, Neurons, Brains=
==''Monday 9/27/10'' - Orientation & Neurons. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
In this first class we will review the basics of neurophysiology with an eye towards what signals of brain function might be visible to the neuroimager. We will discuss information coding, energetics, size and time scales.
[[Image:Neurons.jpg|right]]
''Required Readings''
:*[http://www.ccn.ucla.edu/wiki/images/8/81/The_Active_Brain.pdf The Active Brain]
:*[[media:NeuronFunction+AnatomyNITP.pdf‎| Neuron function slides shown in class]]
:*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]
''Suggested Further Reading''
:*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf "If Neuroimaging is the Answer, What is the Question?" Kosslyn, 1999]
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]
:*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., "Principles of Neural Science"]
:This paper, by Malhi, is a nice orientation in methods of neuroimaging. *[http://www.ccn.ucla.edu/wiki/images/f/f2/Malhi2007.pdf Making sense of neuroimaging in psychiatry]
:*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]

==''Wednesday 9/29/10'' - The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]==
'''A probe mail was sent this afternoon to all students in the class. If you did not receive this (subject, "A Probing Question"), let [mailto:mscohen@ucla.edu me] know'''

We will discuss the general organization of the human brain, and the regional specialization of cortical areas. The emphasis will be on understanding principles of organization:
*Phylogenetic Layering
*Functional Specialization
*Principles Divisions of the Brain
*Brain Systems

''Required Readings''
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[[media:NITPanatomy-Bookheimer.pdf | Slides shown in Class]]
''Suggested Further Reading''

[[media:PNIA2010-PS1.pdf|'''Problem Set 1 Neuroanatomy. Due in class 10/6.''']] Please remember that the preferred way for us to receive problem sets is ''via email'' to [mailto:mscohen@ucla.edu Mark] and to [mailto:alheadbme@ucla.edu Austin].
----
We will be studying linear systems next week. This coming week until Monday would be a good time to review your calculus fundamentals:
:''Derivatives of Polynomials''
:''Integrals of polynomials''
:''Basic trig + derivatives and integrals of sine and cosine functions''

When we start on the linear systems section, we will be using these fundamentals to develop the LaPlace and Fourier transforms, which involve the use of imaginary numbers. The math content for that section is largely contained in this link: [[Media: MathematicalTools.pdf | Mathematical Tools]].

Please let me know by email or other means if this material looks too difficult.

You will need to have matlab installed and running to do the next problem set.

=Week 2: Linear Systems=
Why the emphasis on Linear Systems? Because they are actually ''easy'' (as compared to non-linear systems, which are not.) As we go through this course, we will see many ways in which linear systems theory is applied to:
:Modeling of Neural Systems
:Extraction of Signal from Noise
:Design of Circuits
:Image Enhancement
:Understanding of Image artifacts, and others.

Linear systems analysis is one of the great technologies of the 20th and 21st century. It is now the basis for virtually all electronics design, and its extension into the discrete (digital) domain is the basis for most of modern signal processing.

In our specific case, we will use these few basic principles of linear systems to understand both the instruments we use and the neuroimaging signals we collect. When you have mastered this material, you should be in a much better position to model the systems that you study in order to develop an approach to studying them.

Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer on imaginary numbers] that might be a helpful review.

==''Monday 10/4/10'' - Transforms and the Convolution Theorem. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==

''Required Readings''
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1
:*[[Media: Mathematical_tools.pdf|Mathematical Tools]] - updated 10/4/10 after class

''Suggested Further Reading''
:'''Problem Set 2A - Introduction to matlab'''

''Slides shown in class''
:[[media:LinearityM285.pdf|Linearity and the Fourier Transform]] - updated 10/4/10 after class

Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]

If you are the type who sees beauty in mathematics, the Euler identity may be one of the most beautiful pieces of math in the world.

==''Wednesday 10/6/10'' - Fourier Transform Properties. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
[[Image:xkcd_fourier.jpg|right]]
*Example transform derivations
*The Convolution theorem
*Oddness (and Even-ness)
*The Fourier Shift Theorem
Please see [http://www.brainmapping.org/NITP/PNA/html/ShowConvolutions.html MATLAB demo of Fourier transforms and convolution]

Optional Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 5 through 9
**Note: This reading may be heavy going. I will not be going into nearly this much detail in class, but your time on this will be very well spent. We will be revisiting this material later in the course in week 5.

'''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''
:*[http://www.dspguide.com/CH5.PDF Linear Systems]
:*[http://www.dspguide.com/CH6.PDF Convolution]
:*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]
:''Note: These chapters are lite on math and try to focus on a conceptual understanding''

:'''Problem Set 2B modeling in matlab'''

[[Media: ProblemSet3A.pdf|Problem Set 2A]] and
[http://www.brainmapping.org/NITP/PNA/html/TwoDimensions.html Problem Set 2B]

----

I suggest very strongly that you brush up on linear algebra during this week in anticipation of Dr. Sugar's lectures in statistics. In particular, I would like you to have an understanding of :

:''Matrices as solutions to linear equations - determinants and inverses''
:''Matrix multiplication''

For these, I can recommend the Hefferon text noted above.

=Week 3: Noise and Basic Statistics=
==''Monday 10/11/10'' - Noise. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
It is what you ''don't'' want.
:Additive noise
:White Noise
:Boltzmann noise
:Colored Noise
:Gaussian Noise
:Coherent noise
:Sampling Errors
:Aliasing
:Quantization noise
:Spectral filtering

Noise comes in all shapes and colors. It is present in every measurement we make, from an EEG voltage to an estimate of the effects of dopamine on forebrain signal. Our best weapons are an understanding of the statistical properties of noise, the sources of noise and the ways to control it. Noise in the discrete digital domain is special, as it is both ''created'' by digitization and amplified by sampling.

Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4

:*Slides used in Class:
[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]
:'''Problem set 3 - properties of noise'''

==''Wednesday 10/13/10'' - Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.
[[Image:MeasureForMeasure.jpg|right]]

:*[[media: CohenClassIntroStats10_13_10.pdf | Slides used in class (set 1)]]

''Review of'':
:*Descriptive Statistics: mean, mode, variance, standard deviation
:*Statistical Inference. The Binomial and Normal Distribution
:*Basic Tests: t-test, linear correlation
:*Modeling and non-linear relations
:*Bayes rule

Suggested reading
:*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]
:*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]
:The latter teaches stats at what I feel to be the right level - developing intuitions about the kinds of questions that can be answered using stats and about the statistical tests and measures

:'''Problem Set 5 - Statistics in matlab'''
::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]
::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]

=Week4: Statistics for Imaging=
==''Monday 10/18/10'' - Statistics for Imaging I. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
#Outline
[[image:BVTradeoff.jpg|right]]
''Required Readings''
:*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]

:*The General Linear Model
*Linear Algebra applied to Statistical Solutions
:*Analysis of Variance

''Suggested Further Reading''

==''Wednesday 10/20/10'' - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
*Fixed and Random Effects
*Repeated measures
:*Bonferroni and Other Corrections
*Non-Parametric Methods
*Autocorrelation
*Unknown Distributions

''Required Readings''

''Suggested Further Reading''

=Week 5: Optics=
The prototypical imaging means: Direct visualization. These lectures will cover the principles of light transmission, refraction, reflection and dispersion and will develop a quantitative approach to the analysis of optical systems. We will cover the theory of lenses, imperfections in focus, such as chromatic aberration, and a model of optical devices that builds on our understanding of convolution.
==''Monday 10/25/10'' - Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==
[[Image:Reflection.jpg|right]]
The overall goal of this lecture is to establish that:
''- Physical constants have tangible meanings''
''- Plane waves form a physically unrealizable but extremely good approximation to real systems''
''- Boundaries bend light''
''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''
''- The PSF gives a good indication of the overall performance of an imaging system''
''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''

'''Outline:'''
:* Constitutive parameters (ε, μ, η, n, etc.)
:* Plane wave basics
:* Plane waves at boundaries
:* Lenses
:* Advanced imaging properties of lenses
:* Point spread function.

''Required Readings''
Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].
''Suggested Further Reading''

==''Wednesday 10/27/10'' - Optics II. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==

''Required Readings''

''Suggested Further Reading''

=Week 6: Optical Neuroimaging=
==''Monday 11/1/10'' - Optical Applications. ''Speaker'': tbd==

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/3/10'' - Optical and flourescence methods in dynamic neural systems. ''Speaker'': [mailto:kmcevoy@ucla.edu Kevin McEvoy]==
#Outline
''Required Readings''
:*[http://ccn.ucla.edu/wiki/images/d/d3/NeuroimagingCellularLevel_KMcEvoy_2010.pdf Lecture Slides]

=Week 7: Optical Intrinsic Imaging, Beginning Circuits=
==''Monday 11/8/10'' - Wide field Optical imaging. ''Speaker'': [http://www.uclahealth.org/body.cfm?xyzpdqabc=0&id=479&action=detail&ref=95328 Nader Pouratian]==

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/10/10'' - Circuits I. [http://www.brainmapping.org/MarkCohen Mark Cohen]==
Why circuits?
:(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly
:The device you ''really'' want in your lab doesn't exist. You very well may have to make it.
:There are electronic analogs to most of the linear systems that you have so far studied (and ''vice versa'' - the tools you now understand can be used to analyze and predict circuit behavior).

If you have not had any of this background, you might want to have a look at this handout, [[Media:Electricity.pdf|Electrical Circuits]], in advance. There are near infinite numbers of resources on the web that cover similar material (near enough to infinite that by the time you read all of them, there would be a whole new set.) I have recently come across a link to [http://www.allaboutcircuits.com/ Online Books: All About Circuits] ''IF'' you want practical hands-on knowledge about this material, my all-time favorite text is [http://www.google.com/products/catalog?hl=en&client=safari&rls=en-us&ei=uVSPSfaxE5nMsAPf-tmSCQ&resnum=1&q=art+of+electronics&um=1&ie=UTF-8&cid=8820839049329255765#ps-sellers "Horowitz and Hill: ''The Art of Electronics.''"] The latest edition, however, is dated 1989 and a new third edition is promised. I have therefore stopped short of recommending a purchase unless your need to make circuits is immediate. In this book, you will find an excellent education on the fundamental principles of electrical circuits and an incredible compendium of practical data, such as how to assemble circuit boards, how to make measurements, etc...)

I found a nice [http://video.google.com/videoplay?docid=5645396659673218353&q=Physics+for+Future+Presidents+Electricity&total=5&start=0&num=10&so=0&type=search&plindex=0#0h20m30s intro lecture on charge, current and voltage].

Readings:
:*[[Media: Circuits.pdf|Circuits 1 & 2]]
:*[http://www.brainmapping.org/NITP/PNA/Readings/Circuits.pdf Slides shown in class (''revised 10:30pm 1/28/2010'')]
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10
**You may or may not find this comprehensible without chapters 5 through 9.

We will discuss:
:*Passive Circuit Elements: Resistors, Capacitors, Inductors
:*Gain
:*Transformers
:*Rectifiers
:*Active Elements
::- ''Amplifiers''
::- ''Transistors''
::- ''Op Amps''
:*Solutions with Matrices
''Suggested Further Reading''

=Week 8: Electricity and Electronics. Human Electrophysiology=
==''Monday 11/15/10'' - Electricity and Electronics. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
[[Image:Opamp.jpg|right]]
*Laplace transform analysis
*Op Amp Circuits
*Active Filters
*Noise Control

''Required Readings''

''Suggested Further Reading''
Please note that I have the components we used for the class demos available for you to play with at your leisure.

==''Wednesday 11/17/10'' - Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]==
''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]
*A look at real EEG data
*Preprocessing:
**filtering
**artifact detection/removal
*averaging
*single events
*interpretation

''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]
*Normal and Abnormal EEG
*EEG as a marker for brain state
**sleep staging
**alpha and relaxation
*Neurofeedback???

=Week 9: Practical Electronic Circuits=
This week we will design, build and test a practical device for recording of human electrical potentials: The electromyogram, or EMG. This device must manage the many challenges of interfacing with small biological signals: Sensitivity, Gain, Noise, Linearity, Filtering. The recording we (''hopefully'') will make will demonstrate issues of linearity and neural coding.

==''Monday 11/22/10'' - Design of an EMG Preamp. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
#Outline

''Required Readings''

''Suggested Further Reading''

==''Wednesday 11/24/10'' - Building and Using Electronic Devices: ''EMG''. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
#Outline

''Required Readings''

''Suggested Further Reading''

=Week 10: Filters=
==''Monday 12/1/10'' - Autocorrelation, Filters and Color. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==

''Required Readings''
Most of what we will look at today is in chapter 7 & 8 of Van Drongelen.

''Suggested Further Reading''

==''Wednesday 12/3/10'' - '''Finals Begin'''

File:CohenClassIntroStats10 13 10.pdf

2010-10-21T19:22:37Z

Alhead: First set of slides from Dr. Catherine Sugar's lectures.

First set of slides from Dr. Catherine Sugar's lectures.