will anonymously login the CVS client to the LONI CVS repository "MyProject" (using a blank password--hit return when prompted for a password).
Accessing a Secure CVS Repository
Passwords are not encrypted between a CVS client and a CVS daemon. Therefore a secure connection is required to access a secure CVS repository outside of the LONI local subnet.
Accessing a Secure CVS Repository inside LONI
The CVS daemon can be directly accessed from the LONI local subnet on port 2402. For example:
will login the CVS client "joe" to the LONI CVS repository "MyProject."
Accessing a Secure CVS Repository outside LONI
A secure connection is required to access the CVS daemon outside of the LONI local subnet. Before the CVS daemon can be accessed, an SSH tunnel must be established between the client computer and the LONI CVS computer. A special system user (cvs-ssh) has been created for this purpose. For example:
will establish the SSH tunnel after typing the password !@hss-svc when prompted. The SSH tunnel should be active although there is no further screen output. If the terminal is closed, the SSH tunnel will be stopped. In another terminal, the LONI CVS daemon can be accessed using the CVS client to communicate with the local SSH port. For example:
Create a New System User to Manage the CVS Repository
There should be one system user created to manage each CVS repository. This system user should initially be given exclusive read/write access to all files in the CVS repository. No other system users should be able to read/write files in the CVS repository. It is up to the system user to change the permissions on his/her files if he/she would like to give others access to them.
The system user can be a single user (e.g., rico, neu) if the new CVS repository is intended to store personal files for one user, or it can be a project user (e.g., pipeline, debabeler) if the intention is for multiple clients to share a set of files.
Login as root
Add a new system user
adduser debabeler
passwd debabeler (give the new user a password)
Use the user and group pid of the new system user to add a user entry to /cvs/etc/passwd
Add debabeler:x:506:507::/:/sbin/nologin at the end of /cvs/etc/passwd
Log in as the new system user
ssh cvs.loni.ucla.edu -l debabeler
Edit the .bashrc file in the user's home directory
Add umask 077 at the end of the file
source .bashrc
Initialize the CVS Repository
All CVS repositories are created in the same root directory. The name of each CVS repository should be reflective of the project or user the repository is for.
Do the following as the system user for the new CVS repository:
Change to the main directory for all CVS repositories
cd /cvs/root
Create a directory for the new CVS repository
mkdir Debabeler
cd Debabeler
Initialize the new CVS repository
cvs -d /cvs/root/Debabeler init
Do the following as root:
For a Protected CVS Repository
Add the new CVS repository to those managed by the cvsd daemon
Add Repos /root/Debabeler to the end of /etc/cvsd/cvsd.conf
Restart the cvsd daemon
/etc/init.d/cvsd restart
For an Anonymous CVS Repository
Add the new CVS repository to those managed by the cvsd daemon
Add Repos /root/Debabeler to the end of /etc/cvsd/cvsdAnon.conf
Restart the cvsd daemon
/etc/init.d/cvsdAnon restart
Link the CVS Repository to the LONI User Registration System (CURS)
The CVS password file manages the login names/passwords for all the clients that can access a CVS repository. Do not link an anonymous CVS Repository to the CURS.Do the following as root:
Make the new CVS respository accessible to CURS by adding it to the CURS server group
chmod g+rwx /cvs/root/Debabeler
chgrp 301 /cvs/root/Debabeler
chmod o-rwx /cvs/root/Debabeler/CVSROOT (stop other users from accessing)
chgrp 301 /cvs/root/Debabeler/CVSROOT
Edit the CURS configuration file so CURS knows to update the passwd file
Add /cvs/root/Debabeler/CVSROOT/passwd to the end of /cvs/root/CursUpdates.cfg
Add New User: Determine the new rows added to the application's database tables when a new user is added. Add database inserts to the CURS application page (substituting the CURS name, email, and password).
Is User: Determine how to detect if a CURS user is also an application user. Add database queries to the CURS application page to make the determination.
Sync User: Add database updates to the CURS application page that update the application's encrypted password whenever the CURS password is updated.
Encryption Method
Change the application source code if the application does not encrypt user passwords as CURS does.
Change Password/New User Functionality
Comment out or disable application source code that allows users to register or change passwords via the application.
Application Details
Calendar
account.php (line 106): Remove "create a new account"
Preview your changes to the wiki web page by clicking the rectangular button labelled "Preview Changes"
Once you are satisfied with the web page, save the changes by clicking the "Save Changes" button.
Add a Wiki page
A Wiki web page is considered to describe a specific topic. To add a new topic:
Edit an existing Wiki page and add a WikiWord defining the name of your new Wiki topic.
Preview and Save your changes to the existing web page. Your new Wiki Topic will have a small question mark inserted after the word. This means the new topic has not yet been created.
Click the new topic.
Enter a Wiki user name and password if prompted to do so.
You will be viewing a Wiki Edit web page. Enter the contents of your new topic.
Preview the changes and revise until you are satisfied (see above for details).
* Save the changes to your newly created Wiki Web page.
Adding Images to a Wiki page
*See "Attaching a file to a Wiki page", below.
Attaching a file to a Wiki page.
You may at time want to associate an external file with a Wiki topic.
Examples of this might be to add the detailed agenda of a meeting, or a spreadsheet table containing experimental results,and so forth.
To do so,
Ensure the file is on your local computer.
Click the button labelled "Attach a file". You will be asked to locate the file you want to upload, and to supply a comment that describes the file.
Click the "Upload File" button at the bottom of the upload page.
Your file will be sent to the Wiki web site and a table of file attachments to this web page will appear at the bottom of the web page if it not already there.
If you select the "Link" checkbox before uploading the file and it is an image format recognized by our Wiki software (Twiki) the picture will appear in the web page. You may then Edit the page (see above) if you want to modify the text before the picture, or it's location on the web page.
Deleting an attached file
Locate the attached file in table of files (usually at the bottom of the wiki web page).
Click "Manage"
Click "Move Attachment" (at the bottom of the management web page).
Choose "Trash" from the drop-down Web menu of projects.
Type "TrashAttachment" into the Topic text entry area.
Implement one ITK Segmentation and one ITK Registration Pipeline modules in V.3 and Demo these on Mon 03/20/06.
Specifications
ITK Registration: (please recall that this will require two modules: warping and reslicing!) Read Section 8.4, page 255, (http://www.itk.org/ItkSoftwareGuide.pdf) where the Mutual Information metrics are described. Examples on multimodality registration are available in Insight/Examples/Registration. A demo application using Mutual Information is available under InsightApplications/LandmarkInitializedMutualInformationRegistration. Please read the chapter on image resampling before you get involved with image registration methods. That will save you some problems. Windowed Sync interpolation is always preferred (see p.444, http://www.itk.org/ItkSoftwareGuide.pdf).
Do you feel that researchers are currently happy with the available software for automated brain image analysis (segmentation, registration and labelling)?
Are there specific issues in terms of performance (registration errors, incorrect labelling, segmentation errors) that you are aware of in existing software?
Would users be resistant to the requirement for some level of user interaction to guide segmentation/registration?
What is the most appropriate metric to quantify statistical differences in high-angular resolution diffusion imaging (HARDI) data?
This is a technical question that we are exploring mathematically in many papers, and it is relevant to the registration problem of how to align and statistically compare DTI datasets across subjects (Aim 3). We are interested in feedback from the SAB on how to validate and implement good registration metrics for HARDI. HARDI is exquisitely sensitive to differences in fiber integrity, and extends DTI (diffusion tensor imaging) to even higher angular detail, often using >100 gradient directions to assess diffusion. Having an accurate metric of fiber differences across subjects is central to the problem of HARDI registration (Aim 3). Some issues are: (1) is the dimensionality of the HARDI signal the same everywhere in the brain (no: see Haro et al., 2008); (2) how do you solve the “+ to X” problem – matching fiber crossings across subjects, where the crossings are at different relative angles; (3) how do you define a computational manifold with a metric to detect subtle inter-group differences in fiber integrity (or predict future neurodegeneration, or effects of specific genes on fiber characteristics)? Our stratification maps (Haro et al., 2008) suggest that the variance in the dimensionality of the HARDI signal is much less across subjects at one voxel than across the brain within a subject, so it should be possible to define some powerful metrics to detect abnormalities, so long as the registration problem is solved with a sensible metric.
How do you compute a good statistical power estimate for a project using tensor-based morphometry [or any brain mapping method] (e.g. for use in a drug trial to detect the slowing of Alzheimer’s disease).
This is a key technical question that comes up in several collaborations and is the topic of much debate. In clinical trials, it is typical to estimate the sample size N that would be needed to detect a 25% slowing of the rate of disease progression (as measured by the method, e.g. the rate of regional volume loss in AD), with 80% and 90% power. There is a standard formula for this, based on the means and variances of the rates of progression in each group. In an independent evaluation of the power of our TBM method, Danielle Harvey at UC Davis found that samples of only 123-164 subjects would be needed to detect a 25% slowing of AD, with 80% and 90% power. But, this is likely to be an underestimate of the ultimate power of our method, as it was based on taking the average atrophy rate across the whole temporal lobe, and much more regional (and heterogeneous) changes are occurring. Any ideas for more powerful summary statistics? And, if maps rather than single numbers are used, how should a power estimate be computed to compare degenerative rates? A related open question is how to find the best single numeric measure that can be derived from the TBM maps. [Current ideas: use Hotelling T2 statisics on the deformation tensor Lie group (Roger Woods’ method); compare different deformation priors; or, split the sample to define an a priori region of interest for use in independent samples (e.g., k-fold cross-validation)].
Are there statistical methods not currently proposed for implementation within MAST that should be added?
MAST is primarily conceptualized as a toolkit for morphometric analysis for surface meshes. However, it would be possible to extend its scope to include analysis of voxel-based data, including functional magnetic resonance data. By virtue of the flexible modeling in R, this could potentially offer analysis methods not currently available in standard fMRI analysis packages. Is this something that we should consider implementing within MAST?
Should we widely disseminate the LONI Pipeline outside of neuroimaging (e.g., in bioinformatics)?
There may be pros/cons associated with that (wider recognition, significant burden on maintenance and support, costs, features, infrastructure, etc.)
Infrastructure
Increasing number of requests for collaborations puts a significant strain on our human and computaitonal resources. Demand for support, training and assistance are increasing and our Grid infrastructure is heavily utilized most of the time. How can we mediate some of these demands?
LONIR Principals: Arthur Toga, Paul Thompson, Roger Woods, David Shattuck, Richard Leahy, Jack Van Horn
LONI Collaborators: Liana Apostolova, Ty Cannon, Bob Bilder (UCLA); Judith Rapoport (NIH), Jay Giedd (NIH), Jair Soares (Texas), Russell Jacobs (CalTech), Jim Becker, Pitt
(Distributed the posterlet template, 11/28/06. Posterlets are due 12/19/06 for printing in the LONIR Site-visit Handbook. Here are examples of the Pipeline and Development posters from 2002)
LONI Workbench assists fledgling researchers by giving them a quick‐start introduction into the
realm of neuroscience analysis. The objective of LONI Workbench is to ease the process of
knowledge discovery by sharing or building off of previously published methods and
distributing Pipeline workflows to the public. These workflows are paired with the publications
and methods that they represent and can be downloaded at
http://www.loni.ucla.edu/Research/Publications/.
Elizabeth had her baby on February 27, 2005 at 10:38 pm. His name is James Jackson Crowell, 7 pounds, 1 oz,
20.5 inches. Can't see it in the picture, but he has lots of dark brown hair (hmmm, could he have gotten that from Elizabeth?).
Contact: Elizabeth Sowell
Focus on investigating normal development in children, adolescents, and adults, and identifying abnormalities in pediatric populations.
Read about Edevel
The files in a CVS repository are managed by a system user. The system user controls who can access the files in the CVS repository. In the examples below, the name of the example CVS repository is "MyProject" and the system user that manages it is "myUser".
All the CVS repositories are in the /cvs/root directory. For example:
> ls /cvs/root
drwxrwx--- 3 myUser 301 4096 Jan 18 14:17 MyProject
There are 3 files in the CVS repository that control which clients can read files from the CVS repository, which clients can modify (write) files in the CVS repository, and the access permissions of each client. All 3 files are found in the CVSROOT directory. For example:
/cvs/root/MyProject/CVSROOT
The 3 files are "passwd," "readers," and "writers."
About Passwords
Clients of the CVS repository do not directly access it using the system user. These clients contact the CVS daemon, which accesses the CVS repository on the clients' behalf. The CVS daemon modifies the files in the CVS repository by changing to the system user that is mapped from the client's login name.
The passwd file is a text file that maps each client name/password to a system user name. The format is:
would give joe and betty access to all the files in the CVS repository that the system user "myUser" has access to (joe and betty "become" myUser when they access the CVS repository).
Using CURS passwords
If a client has already registered with CURS (add a new user), the system user for the CVS repository can add the client to the passwd file and allow the client to access the repository using the client's CURS login name and password. For example:
will modify (or create if it does not exist) the file /cvs/root/MyProject/CVSROOT/passwd and add the contents:
joe:Oy.rYAvBGB/Io:myUser
The client must use the CURS login name "joe" to access the CVS repository. Contact the system administrator to make sure that when the client changes his/her CURS password that this passwd file is automatically updated. Once this is set up, do not change the permissions on the CVSROOT directory or the passwd file.
The system user for the CVS repository can also remove a CURS client. For example:
> removeCursClient MyProject joe@loni.ucla.edu
will remove the client with the CURS login name "joe." Or the system user can simply edit the passwd file and remove the line corresponding to the client.
About Readers and Writers
In order to give a client read access to the files in the CVS repository, add the client login name to the "readers" file (create it in /cvs/root/MyProject/CVSROOT if it does not exist). For example:
> more /cvs/root/MyProject/CVSROOT/readers
joe
<-- This line is blank!
gives the client "joe" access to read files. Make sure there is an extra return character at the end of the readers file. If you create a "writers" file and add clients to it in the same way, you are giving the clients read and write access to the files in the CVS repository. But the existence of the writers file leads to a complicated set of rules and may not give expected results. See readers/writers rules for a complete description of what can happen.
Anonymous Access
The files in the CVS repository can be made readable to anonymous users by creating an anonymous CVS client. This is accomplished by adding the line
anonymous:F83DmpZIwYpFw:myUser
(the encrypted password is a blank password--hit return when prompted for a password) to the file /cvs/root/MyProject/CVSROOT/passwd and adding the anonymous login name to the readers file:
> more /cvs/root/MyProject/CVSROOT/readers
anonymous
<-- This line is blank!
Contact the system administrator to make the CVS repository accessible without SSH tunneling.
Create a New User/Group to Manage the CVS Repository
There should be one system user created to manage each CVS repository. This system user should initially be given exclusive read/write access to all files in the CVS repository. No other system users should be able to read/write files in the CVS repository. It is up to the system user to change the permissions on his/her files if he/she would like to give others access to them.
The system user can be a single user (e.g., rico, neu) if the new CVS repository is intended to store personal files for one user, or it can be a project user (e.g., pipeline, debabeler) if the intention is for multiple clients to share a set of files.
Login as root
Add a new system user
adduser debabeler
passwd debabeler (give the new user a password)
Log in as the new system user
ssh cvs.loni.ucla.edu -l debabeler
Edit the .bashrc file in the user's home directory
Add umask 077 at the end of the file
source .bashrc
Initialize the CVS Repository
All CVS repositories are created in the same root directory. The name of each CVS repository should be reflective of the project or user the repository is for.
Do the following as the system user for the new CVS repository:
Change to the main directory for all CVS repositories
cd /cvs/root
Create a directory for the new CVS repository
mkdir Debabeler
cd Debabeler
Initialize the new CVS repository
cvs -d /cvs/root/Debabeler init
Do the following as root:
Add the new CVS repository to those managed by the cvsd daemon
Add Repos /root/Debabeler to the end of /etc/cvsd/cvsd.conf
Restart the cvsd daemon
/etc/init.d/cvsd restart
Link the CVS Repository to the LONI User Registration System (CURS)
The CVS password file manages the login names/passwords for all the clients that can access a CVS repository.
Do the following as root:
Make the new CVS respository accessible to CURS by adding it to the CURS server group
chmod g+rwx /cvs/root/Debabeler
chgrp 301 /cvs/root/Debabeler <--- This will have to be updated for the production server
chmod o-rwx /cvs/root/Debabeler/CVSROOT (stop other users from accessing)
chgrp 301 /cvs/root/Debabeler/CVSROOT <--- This will have to be updated for the production server
LONI Workbench Project Outline LONI Workbench assists fledgling researchers by giving them a quick #8208;start introduction into the realm of neuroscience analysis ...
LONI Projects TABLE{...} Development Edevel Group Contact: Elizabeth Sowell Focus on investigating normal development in children, adolescents, and adults, and identifying ...
Statistics for LONI Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 6072 2 0 1327 ...
Inside LONI LONI Announcements: LONI Community news and events LONI Projects: Group projects under investigation at LONI LONI Technical: LONI Technical LONI FAQ ...
LONI Pipeline V.4.1 Some Thoughts on Functionality Online LONI Calendar Back to Pipeline Meetings Page Missing useful functionality (10/23/08) The features below ...
LONI Resource 2008 Science Advisory Board Members Online LONI Calendar LONI Resource Meetings LONIR SAB Meeting SAB Members Brinkley, James F. brinkley@u.washington ...
LONI Pipeline V.4 Meeting Minutes Thu. 01/17/08, 3:30 PM, DIVE Online LONI Calendar Back to Pipeline meetings page Back to the 01/17/08 Meeting Participants Main ...
Congratulations! It's a boy. Elizabeth had her baby on February 27, 2005 at 10:38 pm. His name is James Jackson Crowell, 7 pounds, 1 oz, 20.5 inches. Can't see it ...
LONI Web Preferences The following settings are web preferences of the LONI web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ...
Accessing an Anonymous CVS Repository The CVS daemon can be anonymously accessed on port 2401. For example: cvs d :pserver:anonymous@cvs.loni.ucla.edu/root/MyProject ...
Adding a New CVS Repository Create a New System User to Manage the CVS Repository There should be one system user created to manage each CVS repository. This system ...
LONI CVS Adding a New CVS Repository Managing a CVS Repository Accessing a CVS Repository General Approach Integrate Users Add New User : Determine the new rows added ...
How To Use the Wiki We encourage you to change the contents of a Wiki web page and to add your own web page topics that is what a Wiki is all about ! Edit a Wiki ...
Upload and revise latest version of the Handbook Mouse manual mouse.doc: Human manual Section A Section A.doc: Overview of data processing and analysis Section B Section ...
LONI R (P41) 2007-2012 LONI SW Tools/Paper Citations Back to LONIR 2007-2012 Outline TOC Software Citations Pipeline : Citations AIR : Citations I Citations II BrainSuite ...
LONI Pipeline Meetings Spring 2006 Pipeline Architecture Design Specs, Docs and Diagrams Online LONI Calendar LONIR Meetings Back to the Spring 2006 Pipeline Meetings ...
LONI Resource 2007 Science Advisory Board (SAB) Meeting VCon/TCon (instead of in person) because of close proximity to the expected P41 site-visit in January 2007 ...
LONI Resource 2008 Science Advisory Board Members Online LONI Calendar LONI Resource Meetings LONIR SAB Meeting SAB Members Brinkley, James F. brinkley@u.washington ...
LONI Workbench Project Outline LONI Workbench assists fledgling researchers by giving them a quick #8208;start introduction into the realm of neuroscience analysis ...
Congratulations! It's a boy. Elizabeth had her baby on February 27, 2005 at 10:38 pm. His name is James Jackson Crowell, 7 pounds, 1 oz, 20.5 inches. Can't see it ...
LONI Projects TABLE{...} Development Edevel Group Contact: Elizabeth Sowell Focus on investigating normal development in children, adolescents, and adults, and identifying ...
LONI Technical Site $ LONI Developers: LONI Developers $ LONI System Administrators : The focus of the System Administration group is on maintaining the computing ...
Managing a CVS Repository The files in a CVS repository are managed by a system user. The system user controls who can access the files in the CVS repository. In ...
Adding a New CVS Repository Create a New User/Group to Manage the CVS Repository There should be one system user created to manage each CVS repository. This system ...
Project Title PI More Project 1 Surface Parameterization Paul Thompson Project 1 Project 2 Volume Parameterization Roger Woods Project 2 Project 3 Feature Extraction ...
Inside LONI LONI Announcements: LONI Community news and events LONI Projects: Group projects under investigation at LONI LONI Technical: LONI Technical LONI FAQ ...
INCLUDINGWEB Web INCLUDINGWEB Web Home Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" warn "Create personal sidebar ...
This is a subscription service to be automatically notified by e-mail when topics change in this LONI web. This is a convenient service, so you do not have to come ...
LONI Web Preferences The following settings are web preferences of the LONI web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ...
TWiki's LONI web SCRIPTURL /view SCRIPTSUFFIX /LONI The LONI web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. INCLUDE{" TWIKIWEB ...
Statistics for LONI Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 6072 2 0 1327 ...
This is a subscription service to be automatically notified by e-mail when topics change in this LONI web. This is a convenient service, so you do not have to come back and check all the time if something has changed. To subscribe, please add a bullet with your WikiName in alphabetical order to this list:
Format: TWiki handles entries in bullet list (<space><space><space>*) format containing the WikiName of a user; a WikiName with e-mail address; or a TWikiGroup. Examples:
Main.FredBloggs
Main.FredBloggs - secondary@home.com
Main.EngineeringGroup
The first entry is the default form, the notification gets sent to the e-mail address specified in the user's home page. The second entry lists an alternative e-mail address. The third entry specifies a group, the notification gets sent to each member of the group.
Related topics:WebChangesAlert, TWikiUsers, TWikiRegistration
The following settings are web preferences of the LONI web. These preferences overwrite the site-level preferences in TWikiPreferences, and can be overwritten by user preferences (your personal topic, eg: TWikiGuest in the Main web).
Preferences:
Loni Customizations
Image, URL and alternate tooltip text of TWiki logo: (can be overwritten by web preferences)
If yes, set SITEMAPLIST to on, do not set NOSEARCHALL, and add the "what" and "use to..." description for the site map. Make sure to list only links that include the name of the web, e.g. LONI.Topic links.
Set SITEMAPLIST = on
Set SITEMAPWHAT = Laboratory of Neuro Imaging Collaboration Platform
Set SITEMAPUSETO = Serve as an intranet for LONI lab members
Exclude web from a web="all" search: (Set to on for hidden webs)
Set NOSEARCHALL =
Prevent automatic linking of WikiWords and acronyms (if set to on); link WikiWords (if empty); can be overwritten by web preferences:
Set NOAUTOLINK =
Note: Use the [[...][...]] syntax to link topics in case you disabled WikiWord linking. The <noautolink> ... </noautolink> syntax can be used to prevents links within a block of text.
Default template for new topics and form(s) for this web:
WebTopicEditTemplate: Default template for new topics in this web. (Site-level is used if topic does not exist)
A preference is defined as: 6 spaces * Set NAME = value Example:
Set WEBBGCOLOR = #FFFFC0
Preferences are used as TWikiVariables by enclosing the name in percent signs. Example:
When you write variable %WEBBGCOLOR% , it gets expanded to #5c79b4 .
The sequential order of the preference settings is significant. Define preferences that use other preferences first, i.e. set WEBCOPYRIGHT before WIKIWEBMASTER since %WEBCOPYRIGHT% uses the %WIKIWEBMASTER% variable.
You can introduce new preferences variables and use them in your topics and templates. There is no need to change the TWiki engine (Perl scripts).
