FUNC: Difference between revisions
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== Getting Started == | == Getting Started == | ||
=== Introduction === | === Introduction === | ||
FUNC is a Computing Cluster | The UCLA FUNC (FUnctional Neuroimaging Core) is a Computing Cluster dedicated to analysis and storage of neuroimaging data. | ||
FUNC is located on the 2nd floor of Franz Hall behind the undergrad computing lounge. | FUNC is located on the 2nd floor of Franz Hall behind the undergrad computing lounge. | ||
: [[FUNC:Detail]] | : [[FUNC:Detail]] | ||
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=== Accessing the Cluster === | === Accessing the Cluster === | ||
How to get on the FUNC (once you have a username/password). | How to get on the FUNC (once you have a username/password). | ||
: [[FUNC: | : [[FUNC:SSH | Using SSH]] | ||
:[[FUNC:NX | Using NX]] | |||
:[[FUNC:VNC | Using VNC]] | |||
=== | === Logging in Remotely === | ||
If you want to access the FUNc from outside the UCLa network you will likely have to install and use the [http://www.bol.ucla.edu/services/vpn/ BOL Virtual Private Network (VPN)]. | |||
: [[ | |||
Once you are connected to the VPN you should be able to use the standard methods to connect to the FUNC (e.g., [[FUNC:NX|NX]], [[FUNC:VNC|VNC]], or [[FUNC:SSH|SSH]]). | |||
=== Data Transfer === | === Data Transfer === | ||
Getting data on the FUNC | Getting data on the FUNC | ||
: [[FUNC:DICOMSERVER | Importing data from the Staglin CCN (dicomserver)]] | |||
: [[FUNC: | |||
: [[FUNC:BMC | Importing data from the Brain Mapping Center (using setup_subject)]] | |||
: [[FUNC:Mount | Mounting the FUNC]] | |||
: [[FUNC: | |||
== Software == | == Software == | ||
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=== NeuroImaging (MR) Analysis Software Packages === | === NeuroImaging (MR) Analysis Software Packages === | ||
==== SPM ==== | ==== SPM ==== | ||
Statistical Parametric Mapping | |||
: [[Hoffman2:MATLAB:SPM]] | : [[Hoffman2:MATLAB:SPM]] | ||
==== AFNI ==== | ==== AFNI ==== | ||
A collection of helpful GUI and programs for functional and structural MR analysis. | |||
[https://afni.nimh.nih.gov/afni/ Official website] | |||
==== FSL ==== | ==== FSL ==== | ||
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. | FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. | ||
: [[Hoffman2:FSL]] | : [[Hoffman2:FSL]] | ||
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official website] | |||
=== Full List of Software === | === Full List of Software === | ||
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=== Scripts === | === Scripts === | ||
Scripts and pipelines available on the FUNC | Scripts and pipelines available on the FUNC | ||
: [[Hoffman2: | : [[FUNC:Scripts]] | ||
== Helpful Resources == | |||
=== Working in a UNIX Environment === | |||
Never heard of a command line before? Vaguely know what "permissions" are and have no idea how to navigate a filesystem? This page is meant to take the scare out of the words "command line" so you can actually use Hoffman2, because no matter how many GUIs there are, command line is king. | |||
: [[Hoffman2:UNIX Tutorial]] | |||
Latest revision as of 01:37, 19 February 2016
**PAGE UNDER DEVELOPMENT**
This page is a resource for FUNC users.
Anyone new to the lab and using FUNC NEEDS to read the first section to have adequate working knowledge of the system.
Getting Started
Introduction
The UCLA FUNC (FUnctional Neuroimaging Core) is a Computing Cluster dedicated to analysis and storage of neuroimaging data. FUNC is located on the 2nd floor of Franz Hall behind the undergrad computing lounge.
Getting an Account
To get an account you should contact Mark Strohm making sure you include your affiliation and the lab/group you are in, and cc-ing your mentor/supervisor. (Note that accounts on the FUNC are currently restricted to UCLA personnel and collaborators.)
Accessing the Cluster
How to get on the FUNC (once you have a username/password).
Logging in Remotely
If you want to access the FUNc from outside the UCLa network you will likely have to install and use the BOL Virtual Private Network (VPN).
Once you are connected to the VPN you should be able to use the standard methods to connect to the FUNC (e.g., NX, VNC, or SSH).
Data Transfer
Getting data on the FUNC
Software
MATLAB
How to use MATLAB on the cluster. It is easier than you think. (Well, maybe...)
NeuroImaging (MR) Analysis Software Packages
SPM
Statistical Parametric Mapping
AFNI
A collection of helpful GUI and programs for functional and structural MR analysis.
FSL
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
Full List of Software
Here you can find a list on what software is available on the FUNC (and sometimes some details on usage).
Productivity
How about streamlining some of those tasks, or getting more things done.
Scripts
Scripts and pipelines available on the FUNC
Helpful Resources
Working in a UNIX Environment
Never heard of a command line before? Vaguely know what "permissions" are and have no idea how to navigate a filesystem? This page is meant to take the scare out of the words "command line" so you can actually use Hoffman2, because no matter how many GUIs there are, command line is king.