Center for Cognitive Neuroscience - User contributions [en]

User:Jpdiaz

2022-08-24T03:15:24Z

Jpdiaz: add website info

https://orcid.org/0000-0002-2108-6830

https://www.JOEwithanL.com

Where to order EEG supplies

2022-08-24T03:14:01Z

Jpdiaz: new sales email for egi

We have had success ordering supplies from the following places. The ones ordered from online sites accept purchase orders:
*'''Pipettes''' (5.8mL, non-sterile) - [http://www.fishersci.com/ecomm/servlet/fsproductdetail?storeId=10652&productId=634785&catalogId=29104&matchedCatNo=1371120||137119AM||137119CM||137119BM&fromSearch=1&searchKey=pipette||pipettes||pipeters||pippette||pipettor||pipetter||pipeter||pipettors||pipetters&highlightProductsItemsFlag=Y&endecaSearchQuery=%23store%3DScientific%23nav%3D0%23rpp%3D25%23offSet%3D0%23keyWord%3Dpipettes%23searchType%3DPROD%23SWKeyList%3D Fisher Scientific]
*'''MT Spandages''' (MT07, 7-inch spandage, 25 yards) - [http://www.vitalitymedical.com/mt-spandage-tubular-elastic-dressing.html Vitality Medical MT Spandage]
*'''Johnson & Johnson Baby Shampoo''' - please send a purchase request to the [https://www.semel.ucla.edu/staglin/contact CCN Administrator] [https://www.johnsonsbaby.com/baby-products/johnsons-baby-shampoo?upcean=381371025619]
*'''EGI Potassium Chloride (KCl)''' (2Lb) - E-mail: [mailto:sales@magstimegi.com sales@magstimegi.com] [https://www.egi.com/order-supplies]
*'''Control III Disinfectant''' (16 oz. bottle) - E-mail: [mailto:control3@earthlink.net control3@earthlink.net] [http://www.controlthree.com/contact-us.html]
*'''GSR Electrodes''' (EL509, 100 electrodes/box) - [http://www.biopac.com/disposable-radiotranslucent-dry-electrode Biopac Systems, Inc.]
*'''Self-Adhesive Bandage''' (Item 2082, 2-inch x 5 yards, latex-free) - [http://www.vitalitymedical.com/coban-self-adherent-wrap.html Vitality Medical Self-Adhesive Wrap]

<div style="text-align: center; border: 1px dotted gray;">Return to the [[Staglin EEG Suite]] main page</div>

New User Checklist

2022-07-18T18:31:31Z

Jpdiaz: add new user checklist

Below is a general checklist of items to complete for incoming staff and students.

#Register for a g.ucla.edu (google) account:
#*https://g.ucla.edu/
#Install and configure VPN on your personal computer:
#*https://it.ucla.edu/it-support-center/services/virtual-private-network-vpn-clients
#Complete CITI research training:
#*https://ohrpp.research.ucla.edu/citi-training/
#If your lab uses the Hoffman2 cluster for data processing:
##Register for a Hoffman2 account:
##*https://www.hoffman2.idre.ucla.edu/Accounts/Requesting-an-account.html
##Download X2Go:
##*https://wiki.x2go.org/doku.php/doc:installation:x2goclient
##Configure X2Go for remote desktop access to Hoffman2:
##*https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html#x2go-client
#Complete any UCLA Health training certifications listed under “My Transcript” (requires AD/Mednet ID):
#*https://uclahealth.csod.com/samldefault.aspx
#Complete MRI and/or EEG Certification

Main Page

2022-07-18T17:58:54Z

Jpdiaz: /* Resources */ add new user checklist

__NOTOC__
== Center for Cognitive Neuroscience at UCLA ==

Welcome to the Wiki of the Center for Cognitive Neuroscience at UCLA (CCN at UCLA). Please find and contribute helpful information for lab usage here.

=== Classes ===
* [[CCN Workshops]]
* [[Neuroimaging+ Journal Club]]
* [[Principles of Neuroimaging - 2016-2017]]
* [[Principles of Neuroimaging - 2015-2016]]

=== Computing ===
* [[Hoffman2 maintenance and Issues]]
* [[Hoffman2]]
* [[Dicom]]
* [[Psychophysics]]


=== EEG/fMRI ===
* [[EEG]] (includes EEG-fMRI)
* [[MR]]


=== Staglin Center ===
* [[Staglin EEG Suite]]
* [[Staglin MR Suite]]
*Staglin Ultrasound Suite

=== Resources ===
* [[New User Checklist]]
* [[Software Licenses]]


===Instructions For Admins ===
* [[Instructions]]

Hoffman2:FSL

2022-07-15T19:56:20Z

Jpdiaz: add fsl gpu example

[[Hoffman2|Back to all things Hoffman2]]

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:
* do nothing, and always use the "current" version of FSL on the cluster
* [[Hoffman2:Modules#FSL|actively choose]] which version of FSL you would like to run
We recommend the latter for data integrity and reproducibility.

==FSL GUI==
Make sure you source the FMRI Path in your [[Hoffman2:Profile | Profile]] before doing anything, or else you won't be able to access FSL.

To run FSL using a GUI on hoffman2, use the following command:
$ fsl &

If you received this message while opening FSL
DISPLAY is not set. Please set your DISPLAY environment variable!

It means you did not open X11 along with your ssh connection. See [[Hoffman2:Accessing_the_Cluster#GUI-Enabled_SSH_.5BRecommended.5D | here]] for more information.

==FSL TOOLS==
A complete list of tools can be found [http://www.fmrib.ox.ac.uk/fsl/fsl/list.html here]

Functional MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fabber/index.html fabber]
| Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.
|}

Structural MRI (command line only)
{| class="wikitable"
|-
! Tool
! Explanation
|-
| [http://www.fmrib.ox.ac.uk/fsl/bet2/index.html bet]
| Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fast4/index.html fast]
| FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.
|}

GUI Commands/Tools [Make sure to have X11 forwarding on]
{| class="wikitable"
|-
! Tool
! Explanation
|-
| fsl
| Bring you to the FSL menu where you can choose what type of analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.
|-
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
|-
| [http://www.fmrib.ox.ac.uk/fsl/feat5/featquery.html Featquery]
| A program which allows you to interrogate FEAT results by defining a mask or set of co-ordinates (in standard-space, highres-space or loweres-space) and get mean stats values and time-series.
|-
| Glm
| A GUI for setting up just the design matrix and contrasts, in the same way as in FEAT, for use with other modelling/inference programs such as randomise.
|-
| [http://www.fmrib.ox.ac.uk/fsl/melodic/index.html Melodic]
| Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
|-
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
| Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..
|-
| Renderhighres
| Transforms all thresholded stats images in a FEAT directory into high resolution or standard space and overlays these onto the high resolution or standard space images. This then produces PNG format pictures of the overlays and, by default, deletes the 3D AVW colour overlay images.
|-
| [http://www.fmrib.ox.ac.uk/fsl/miscvis/index.html Renderstats]
| This tool allows you to combine a background image (raw FMRI or high resolution MRI) image with one or two statistics images. The statistics image(s) must be in registration with the background image.
|-
| [http://www.fmrib.ox.ac.uk/fsl/susan/index.html Susan]
| Nonlinear noise reduction.
|-
| [http://www.fmrib.ox.ac.uk/fsl/fslview/index.html fslview]
| Interactive display tool for 3D and 4D data.
|}

==Cluster==
{| class="wikitable"
|-
! Scripts that self-submit
|-
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html feat]
| [http://www.fmrib.ox.ac.uk/fsl/first/index.html first]
| [http://www.fmrib.ox.ac.uk/fsl/fslvbm/index.html fslval]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html possom]
| [http://www.fmrib.ox.ac.uk/fsl/randomise/index.html randomise]
| [http://www.fmrib.ox.ac.uk/fsl/tbss/index.html tbss]
|-
! GUIs that self-submit
| [http://www.fmrib.ox.ac.uk/fsl/fdt/index.html Fdt]
| [http://www.fmrib.ox.ac.uk/fsl/feat5/index.html Feat]
| [http://www.fmrib.ox.ac.uk/fsl/flirt/index.html Flirt]
| [http://www.fmrib.ox.ac.uk/fsl/possum/index.html Possum]
|-
|-
|-
|}

FSL_SUB




==NO_FSL_JOBS==
Sometimes FSL doesn't know how to allocate enough resources for its jobs properly. Specifically we have found the FEAT tool often unable to do this for group analyses or other complex tasks. So we did some tinkering with FSL to allow you to override its job submission on Hoffman2 and run it like it was just on your laptop. '''The trick is to set <code>NO_FSL_JOBS=true</code> in your environment and FSL will not submit jobs.'''

===Interactive Session===
If you want to watch FEAT run (kinda like paint drying, but to each their own), you can do the following
#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line|SSH]] into the cluster
#Check out an [[Hoffman2:Interactive_Sessions|interactive node]] with the necessary time and memory
#*<code>qrsh -l h_rt=3:00:00,h_data=4G</code>
#Set the environment variable
#*<code>export NO_FSL_JOBS=true</code>
#Run your FSL commands. '''This means not using qsub, or command files, but simply executing the FSL command'''
#The commands will just run and not submit any jobs.

===Submitting a Job===
If you don't want to watch FEAT run (why would you?), you can do the following

Create a shell script (e.g. myshellscript.sh) with the following contents
#!/bin/bash
export NO_FSL_JOBS=true
feat design.fsf
# any other FSL commands you want

And make sure to run <code>chmod 750</code> to make the script executable
chmod 750 myshellscript.sh

Submit the shell script [[Hoffman2:Submitting_Jobs|as a job]] but with the adequate time and memory allocations
qsub -l h_rt=23:00:00,h_data=4G -V -m bea -cwd /path/to/myshellscript.sh

And the FSL commands will be sent into the queue to run with your time and memory constraints rather than FSL's. This may take some playing with to get the time and memory allocations correct, but at least you have the ability to tweak them.

==FSL GPU==

Some FSL tools, like ''eddy'' and ''bedpostx'', can utilize Hofmman's GPU architecture to speed up their processing times. Below is an example of how to request a CUDA 9.1-enabled GPU node.

# request Tesla P4 GPU node
qrsh -l gpu,P4,h_rt=5:00:00

module load cuda/9.1
module load fsl/6.0.4
export NO_FSL_JOBS=true

# now run eddy_cuda9.1 or bedpostx_gpu

==External Links==
* Official FSL website http://www.fmrib.ox.ac.uk/fsl/

StaglinCenter:EEG-FMRI

2022-07-14T16:40:43Z

Jpdiaz: Moving supplies list from MR page to EEG-FMRI page

==EEG-FMRI Experiments==
*[[StaglinCenter:EEG-FMRI:AVTask]]

== Supplies ==
=== Where to order supplies ===
*'''GSR electrodes''' (EL509, 100 electrodes/box): [http://www.biopac.com/disposable-radiotranslucent-dry-electrode Biopac Systems, Inc.]
*'''Self-adhesive wrap''' (Coban tan wrap, item # 2082, 2 in x 5 yardm 36 rolls/box): [http://www.vitalitymedical.com/coban-self-adherent-wrap.html Vitality Medical]

Hoffman2:Software Tools

2022-05-14T00:23:58Z

Jpdiaz: add mriqc and adjust page format

[[Hoffman2|Back to all things Hoffman2]]

There is a CCN usergroup on Hoffman2 which is maintained for groups doing Neuroimaging work at UCLA. Tools like FSL, FreeSurfer, AFNI and Nibabel are maintained for this group separate from normal Hoffman2 programs. In order to take advantage of these tools, you need to load the modules into the interactive mode or listed in your batch mode scripts.

module load appname/version

Below is a list of the available software tools. We will do our best to update it as changes are made.

==AFNI==
[http://afni.nimh.nih.gov/afni/ Official Webste]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
|20.1.00 || || New
|- class="ccn-table-odd"
|19.0.15 || 2019.02.20 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
|17.2.07 || 2017.02.07 || Default
|- class="ccn-table-odd"
|16.3.1 || 2016.11.20 ||
|- class="ccn-table-even""
|2011.12.21.1014 ||2012.03.19 ||
|}

==ANTS==
[http://stnava.github.io/ANTs/ Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
|ants-2.3.1 || || New
|- class="ccn-table-odd"
|ants-2.2.0 || 2019.03.25 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
|ants-2.1.0-redhat || 2015.01.23 || Default
|}

==ASHS==
[https://www.nitrc.org/projects/ashs| Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 20180720 || 2018.07.20 || New
|- class="ccn-table-odd"
| 2017-02 || 2017.06.08 ||
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| Rev-103 || 2016.02.24 || Default
|}

==BrainSuite==
[http://brainsuite.org/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 19a || 2019.02.19 || Default
|- class="ccn-table-odd"
| 18a || ||
|- class="ccn-table-even"
| 17a || ||
|- class="ccn-table-odd"
| 15c || 2016.02.18 || No longer supported
|}



==Caret==
[http://brainvis.wustl.edu/wiki/index.php/Caret:About Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 5.65 (2012.01.27) || 2013.07.15 || Default, not folded into the main profile
|}

==ccn_py37==
Conda virtual environment with nibabel, nilearn, pydicom, pandas, scikit-learn, scipy

[[Hoffman2:Software Tools:ccn_py37|How to load]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 1.0 || 2021.05.24 || CentOS 7 with Conda
|}

==Chronux==
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 2.10 || 2013.02.26 || Current
|}

==CONN==
[https://web.conn-toolbox.org/ Official Website]

[[Hoffman2:Software Tools:CONN|Load CONN module]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 19.b || || New
|- class="ccn-table-odd"
| 18.b || ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 17.f || || Default
|}

==dcm2nii==
[http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html Official Website]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 2013.06.06 || 2014.03.06 ||
|- class="ccn-table-even"
| 2011.11.11 || circa 2011 || Current
|}

==dmctk==
[https://dicom.offis.de/dcmtk.php.en Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 3.6.0 || 2017.05.17 || Current
|- class="ccn-table-even"
| 3.6.6 || 2021.02.16
|}

==DTIprep==
[https://www.nitrc.org/projects/dtiprep/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.2.4 || 2017.12.21 ||
|- class="ccn-table-even"
| 1.2.9 || 2018.03.20 || Current
|}

==EEGLAB==
[http://sccn.ucsd.edu/eeglab/ Official Website]

[http://sccn.ucsd.edu/wiki/EEGLAB_revision_history Release Notes]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 13.1.1b || 2014.01.29 ||
|- class="ccn-table-even"
| 12.0.2.5b || 2013.11.14 ||
|- class="ccn-table-odd"
| 11.0.5.4b || 2013.11.14 ||
|- class="ccn-table-even"
| 12.0.0.0b || 2012.12.10 ||
|- class="ccn-table-odd"
| 11.0.0.0b || 2012.02.21 ||
|- class="ccn-table-even"
| 10.2.5.8b || 2012.02.21 ||
|}

==ENIGMA==
[https://www.nitrc.org/projects/dtiprep/ Official Website]

[[Hoffman2:Software Tools:Enigma|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 20210422 || 2021.04.22 || Current
|}

==ENIGMA HALFpipe==
[https://github.com/HALFpipe/HALFpipe Official Website]

[[Hoffman2:Software Tools:HALfpipe|Usage]]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.1.1 || 2021.08.27 || Current
|}

==FastSurfer==
[https://github.com/Deep-MI/FastSurfer/ Official Website]

[[Hoffman2:Software Tools:FastSurfer|Usage]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 202102 || 2021.03.01 || Current
|}

==FIT==
[https://trendscenter.org/software/fit/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| FITv2.0d || 2021.01.13 ||
|- class="ccn-table-even"
| FITv2.0e || 2021.01.13 ||
|}

==FIX==
[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide Official Website]

[[Hoffman2:Software Tools:Fix|Use Fix in Hoffman]]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.06.15 || 2021.12.01 ||
|}

==FMRIprep==
[https://fmriprep.readthedocs.io/en/stable/usage.html Official Website]

[[Hoffman2:Software Tools:FMRIprep|Load pre-requisite modules]]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 20.2.1 ||2021.05.13 || In Singularity
|- class="ccn-table-even"
| 20.2.0rc0 || ||
|- class="ccn-table-odd"
| 20.1.1 || || * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-even"
| 1.4.0 || 2019.01.11 || Default * [[#Known_issue_2 |known Issue ]]
|- class="ccn-table-odd"
| 1.3.2 || 2019.01.11 || * [[#Known_issue_2 |known Issue ]]
|}

<div id="Known_issue_2" style="display:inline;">Known issues: please see [https://github.com/nipreps/fmriprep/blob/master/.versions.json version history] </div>

==FreeSurfer==
[http://surfer.nmr.mgh.harvard.edu/ Official Website]

[http://freesurfer.net/fswiki/ReleaseNotes Release Notes]
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 7.2.0 || 2021.11.29 ||
|- class="ccn-table-odd"
| 7.1.1 || 2021.02.26 ||
|- class="ccn-table-even"
| 6.0.0 || 2017.01.18 || CentOS 6 only
|}



==FSL==
[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Official Website]

[http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew Revision History]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes

|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 6.0.4 || 2021.01.25|| new
|- class="ccn-table-odd"
| 6.0.3 || 2021.09.30||
|- class="ccn-table-even"
| 6.0.1 || 2019.03.01 ||
|- class="ccn-table-odd"
| 6.0.0 || 2018.10.23 ||
|- class="ccn-table-even"
| 5.0.11 || 2018.03.19 ||
|- class="ccn-table-odd"
| 5.0.10 || 2017.04.24 || * [[#Known_issue_1 |Known Issue ]]
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 5.0.9 || 2015.10.02 || Default
|- class="ccn-table-odd"
| 5.0.8 || 2014.12.03 ||
|- class="ccn-table-even"
| 5.0.7 || 2013.10.17 ||
|- class="ccn-table-odd"
| 5.0.6 || 2013.12.18 || (2013.12.18-2014.10.10)
|- class="ccn-table-odd"
| 4.1.9 || 2011.12.01 ||
|- class="ccn-table-even"
| 4.0.4 || circa 2008 ||
|}

<div id="Known_issue_1" style="display:inline;">Known issue: 5.0.10 fsleyes crash on x2go</div>

==gift==
[https://trendscenter.org/software/gift/ Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| GroupICATv4.0b || 2017.11.14 ||
|- class="ccn-table-even"
| GroupICATv4.0c || 2021.01.04 ||
|}

==gradunwarp==
[https://github.com/Washington-University/gradunwarp Official Website]

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-odd"
| 1.1.0 || 2019.06.04 ||
|}

==HCP Benchwork ==
[https://www.humanconnectome.org/software/connectome-workbench Official Website]
* Note: module name: hcp
{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 1.3.2 || 2019.05.22 || New
|- class="ccn-table-odd"
| 1.2.3 || 2018.02.13 ||
|- class="ccn-table-even" style="background-color:#ffffcc;"
| 1.1.1 || 2016.02.18 || Default
|- class="ccn-table-odd"
| 1.0 || ||
|- class="ccn-table-even"
| 0.84 || ||
|}

==ICA-AROMA==

{| class="wikitable"
! class="ccn-table-header" | Version
! class="ccn-table-header" | Install Date
! class="ccn-table-header" | Notes
|- class="ccn-table-even" style="background-color:#E5FFCC;"
| 0.4.5 || || New
|- class="ccn-table-odd" style="background-color:#ffffcc;"
| 0.4.1-beta || || Default
|}

* Note: Python 2.7 available for v0.4.5, module name: ica-aroma_py27.
[[Hoffman2:Software Tools:ica-aroma_py27|Load ica-aroma_py27 module]]

==ITKGray==
[http://vistalab.stanford.edu/newlm/index.php/ItkGray Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 080803 || 2009.11.19 || Default
|- class="ccn-table-even"
| 080128 || 2009.11.13 ||
|}

==ITKSnap==
[http://www.itksnap.org/pmwiki/pmwiki.php Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 3.4.0.QT4 || 2016.02.24 || Default
|- class="ccn-table-even"
| 3.6.0.QT4 || 2021.03.02 ||
|- class="ccn-table-odd"
| 3.8.0.QT4 || 2021.03.02 || Default
|}

==kwave==
[http://www.k-wave.org/doxygen/index.html Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 1.3 || 2020.07.20 || Current
|}

==MANGO==

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 20190905 || || Current
|}

==MRIQC==
[https://mriqc.readthedocs.io/en/latest/ Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.16.1 || 2021.03.08 || Current
|}

==NDATools==
[https://github.com/NDAR/nda-tools Official Website]

[[Hoffman2:Software Tools:NDATools|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.2.3 || 2021.03.04 || Current
|}

==OpenSmile==
[https://www.audeering.com/opensmile/ Official Website]

[[Hoffman2:Software Tools:OpenSmile|Usage]]
{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 3.0.0 || 2021.03.23 || Current
|}

==Profumo==
[https://git.fmrib.ox.ac.uk/samh/profumo Official Website]

[[Hoffman2:Software Tools:Profumo|Usage]]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 0.11.3 || 2021.06.22 || Current
|}



==RATS==
[https://www.iibi.uiowa.edu/rats-rodent-brain-mri/ Official Website]

{| class="wikitable"
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| 060419 || 2019.06.04 || Current
|}

==SPM==
[http://www.fil.ion.ucl.ac.uk/spm/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Last Patch Applied
! class="ccn-table-header"| Last Checked Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| SPM12-standalone || || || Current
|- class="ccn-table-even"
| SPM12 || || ||
|- class="ccn-table-odd"
| SPM8 || 5236 || 2014.01 ||
|- class="ccn-table-even"
| SPM5 || Unknown || N/A || No longer supported
|}

==TrackVis/Diffusion Toolkit==
[http://trackvis.org/ Official Website 1]

[http://trackvis.org/dtk/ Official Website 2]
{| class="wikitable"
! class="ccn-table-header"| Tool
! class="ccn-table-header"| Version Number
! class="ccn-table-header"| Last Checked Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd"
| TrackVis || 0.5.2.2 || 2014.03.06 ||
|- class="ccn-table-even"
| Diffusion Toolkit || 0.6.2.2 || 204.03.06 ||
|}

==WEKA==
[http://www.cs.waikato.ac.nz/ml/weka/ Official Website]
{| class="wikitable"
! class="ccn-table-header"| Version
! class="ccn-table-header"| Install Date
! class="ccn-table-header"| Notes
|- class="ccn-table-odd" style="background-color:#E5FFCC;"
| 3.8.1 || ||
|- class="ccn-table-odd"
| 3.7.10 || 2014.03.03 ||
|- class="ccn-table-even"
| 3.6.5 || circa 2011.08 ||
|}



==External Links==
*[https://www.hoffman2.idre.ucla.edu/software/ Other Hoffman2 Software]

Main Page

2022-02-11T21:36:56Z

Jpdiaz: /* Center for Cognitive Neuroscience at UCLA */ add resources section

__NOTOC__
== Center for Cognitive Neuroscience at UCLA ==

Welcome to the Wiki of the Center for Cognitive Neuroscience at UCLA (CCN at UCLA). Please find and contribute helpful information for lab usage here.

=== Classes ===
* [[CCN Workshops]]
* [[Neuroimaging+ Journal Club]]
* [[Principles of Neuroimaging - 2016-2017]]
* [[Principles of Neuroimaging - 2015-2016]]

=== Computing ===
* [[Hoffman2 maintenance and Issues]]
* [[Hoffman2]]
* [[Dicom]]
* [[Psychophysics]]


=== EEG/fMRI ===
* [[EEG]] (includes EEG-fMRI)
* [[MR]]


=== Staglin Center ===
* [[Staglin EEG Suite]]
* [[Staglin MR Suite]]

=== Resources ===
* [[Software Licenses]]

Resources at UCLA

2022-02-11T21:36:08Z

Jpdiaz: update resources page and publish as active

== Resources for Students, Staff, & Faculty at UCLA ==

Below is a non-exhaustive list of campus-wide software licenses available to UCLA students, faculty, and staff.

For up-to-date information, please visit the [https://www.digitaltoolkit.ucla.edu/ UCLA Digital Toolkit], the
[https://ucla.service-now.com/support?id=kb_view UCLA IT Services Knowledge Base], and the [https://softwarecentral.ucla.edu/ UCLA Software Central]. - {{last edited by|brief=yes}}

=== Google Apps for UCLA ===
* [https://g.ucla.edu/ g.ucla.edu]
** Generally required for access to UCLA licensed software.
** Includes Unlimited Cloud Storage with Google Drive.

=== Office 365 ===
* Microsoft Office ProPlus (Students)

=== Box ===
* [https://ucla.service-now.com/support?id=its_browse_service&sys_id=cb31ebb01b9c885038cec8415b4bcb9a Box] - Unlimited Cloud Storage Solution
** General Purpose (g.ucla.edu): https://ucla.account.box.com/
** HIPAA-compliant (mednet): https://uclahs.account.box.com/

=== MATLAB ===
* Academic Licenses
* https://softwarecentral.ucla.edu/matlab-getmatlab
* https://www.mathworks.com/academia/tah-portal/ucla-31454052.html

=== Collaboration Tools ===
* '''Slack'''
** [https://ucla.slack.com/ ucla.slack.com]

* '''Zoom'''
** General Purpose (g.ucla.edu): https://ucla.zoom.us/
** HIPAA-compliant (mednet): https://ucla-hipaa.zoom.us

=== Security Software ===
* [https://frontdoorsoftware.com/UCLA/ '''FrontDoorSoftware''']
** Loss, Recovery and Personal Safety Software
** Available for up to four years

=== References ===
* https://softwarecentral.ucla.edu/
* https://www.it.ucla.edu/it-support-center
* https://www.it.ucla.edu/connect-at-home

Software Licenses

2022-02-11T21:18:30Z

Jpdiaz: redirect to Resources at UCLA

#REDIRECT [[Resources at UCLA]]

Hoffman2

2022-02-11T21:11:41Z

Jpdiaz: /* Software */ add git page with redirect to "Setting Up and Using Git"

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



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

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

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

=== Working in a Linux 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.
: [[Hoffman2:Linux Tutorial]]

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

=== Environmental Modules ===
How to get access to CCN-supported software.
: [[Hoffman2:Modules]]

=== Changing Passwords ===
How to change your Hoffman2 password.
: [[Hoffman2:Changing Passwords]]

=== Password-less Logins ===
Log in to Hoffman2 without typing your password every time.
: [https://www.hoffman2.idre.ucla.edu/About/FAQ/FAQ.html#set-up-ssh-public-key-authentication Password-less ssh]

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

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

=== Run Your Jobs ===
You can run your job by starting an interactive session or submitting it with batch mode.


:[[Hoffman2:Interactive_Sessions]]
:[[Hoffman2:Batch Mode]]
:[[Hoffman2:Job Array]]

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



== Software ==
=== MATLAB ===
How to use MATLAB on the cluster. It is easier than you think. (Well, maybe...)
: [[Hoffman2:MATLAB]]
: [[Hoffman2:parpoolexample.m]]

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

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

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

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

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

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

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

=== Python ===
: [[Hoffman2:Python]]

=== Jupyter Notebook ===
: [[Hoffman2:JupyterNotebook]]

=== Singularity ===
: [[Hoffman2:Singularity]]

=== Git ===
: [[Hoffman2:Git]]

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

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

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

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

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

=== Mailing List ===
Information about the the CCN-Hoffman mailing list, including how to join the list.
: [[Hoffman2:Mailing List]]

Hoffman2:Git

2022-02-11T21:07:27Z

Jpdiaz: redirect to "Setting Up and Using Git" page

#REDIRECT [[Setting Up and Using Git]]

ICLabel

2022-01-12T19:05:31Z

Jpdiaz: /* How to properly install ICLabel on Hoffman */

==How to properly install ICLabel on Hoffman==
After downloading ICLabel and placing it in the eeglab plugins folder, MatConvNet should be compiled for optimal CPU computations.

First, request an interactive session, then load the required software:
# load env
module load gcc/4.9.3 # 4.8 or newer
module load matlab # R2015b or newer

# open matlab
matlab &

Once Matlab is open, change the directory to the MatConvNet folder and compile the library using the following:
% compile matconvnet
cd eeglab/plugins/ICLabel1.2.6/matconvnet
addpath matlab

% configure mex to use 'g++'
mex -setup C++
vl_compilenn('verbose', 1)

% test library
vl_testnn

===Resources===
*[https://labeling.ucsd.edu/tutorial ICLabel]
*[https://www.vlfeat.org/matconvnet/install/ MatConvNet]

Psychophysics

2022-01-12T19:03:13Z

Jpdiaz: /* Python */ add info for hardware IO

==MATLAB==
*[http://psychtoolbox.org/ Psychophysics Toolbox Version 3 (PTB-3)]
* Hardware IO:
** [http://psychtoolbox.org/docs/NetStation NetStation]
*** Wrapper to interface with NetStation (uses NTP to synchronize with a NetStation amplifier).
** [http://psychtoolbox.org/docs/Eyelink Eyelink]
*** Wrapper for the EyeLink eye tracker.
** [https://github.com/esdalmaijer/EyeTribe-Toolbox-for-Matlab EyeTribe Toolbox]
*** Wrapper for the EyeTribe eye tracker. Relies on pytribe scripts.

==Python==
*[https://www.psychopy.org/ PsychoPy]
*[https://osdoc.cogsci.nl/ OpenSesame]
* Hardware IO:
** [https://egi-pynetstation.readthedocs.io/en/latest/# egi-pynetstation]
*** Wrapper to interface with NetStation (uses NTP to synchronize with a NetStation amplifier).
** [https://www.sr-support.com/thread-48.html pylink]
*** Wrapper for the EyeLink eye tracker.
** [https://github.com/esdalmaijer/PyTribe pytribe]
*** Wrapper for the EyeTribe eye tracker.

==JavaScript==
*[https://www.jspsych.org/ jsPsych]
*[https://lab.js.org/ lab.js]
*OSWeb/OpenSesame
*[https://www.psytoolkit.org/ PsyToolkit]

==Web-Based Experiments==
*[https://pavlovia.org/ Pavlovia]
*[https://www.jatos.org/ JATOS]
*[https://gorilla.sc/ GORILLA]

==Other==
*E-Prime
*Presentation
*Experiment Builder (SR Research)

Staglin MR Suite

2022-01-12T18:49:25Z

Jpdiaz: /* Peripheral Equipement */ update equipment info

==MRI Facilities & Equipment==

===Scanning Facilities===
The Staglin IMHRO Center for Cognitive Neuroscience operates a Siemens 3 Tesla Prisma Fit MRI Scanner equipped with 20, 32, and 64 channel head coils.

===Peripheral Equipement===
Peripheral equipment available for projects include:
*Siemens headphone/speak system,
*Siemens physiological measurement system,
**Includes pulse, respiration, and EKG.
*[http://www.mrivideo.com/visuastimdigital.php VisuaStim digital system] by RTC,
**Includes goggles/headphone/controller unit.
*[http://www.optoacoustics.com/medical/optoactive-ii Optoacoustics] noise-canceling headphones and microphone,
*[http://www.crsltd.com/boldscreen24 BOLDscreen 24" LCD Display],
**LCD projection system controlled via fiberoptic cabling.
*4-button and 2-button response pads by Current Designs,
*32 channel electronic interface and power supply unit, and
*[https://www.biopac.com/wp-content/uploads/MP150-Systems.pdf BIOPAC MP150]
**For collecting physiological measures.
**Includes skin conductance, respiration rate, and pulse rate/waveform.

===Multimodal Data Collection===
*[https://www.ccn.ucla.edu/wiki/index.php/StaglinCenter:EEG-FMRI Concurrent EEG]
*[[Low Frequency Focused Ultrasound]]
*[[Eye Tracking]]

===Dedicated iMac Computer===
The MR suite is equipped with a dedicated iMac computer with a dual-boot Windows partition, currently running:
*Psychophysics Software:
**Psychtoolbox,
**PsychoPy,
**E-Prime,
*MATLAB 2015b
*AcqKnowledge 4 (for BioPac MP150)
*[[FIRMM]]

For new software, please contact the MR Technician before installation.

== How to record EKG using the Siemens built-in system ==
The Siemens Trio Scanner comes with its own EKG monitoring system which wirelessly transmits the patient EKG signal to the recording computer.

=== Setting up the EKG ===
The same principles of EKG prep hold true, except there are three leads: Right Arm, Right Leg and Left Leg
# Prepare the areas by wiping them down with an alcohol wipe
# Scrub the areas with a cotton swab using NuPrep
# Re-clean the area with an alcohol wipe and allow to dry
# Apply lead stickers to each of the areas and connect the proper EKG leads to them, they are labeled:
*RA - Right Arm
*RL - Right Leg
*LL - Left Leg
# Tape down the EKG leads so they stay connected to the stickers.
# Tape down the wireless device box so it doesn't move.
# Prep the subject for EEG

=== Setting up the Scanner ===
'''STILL TESTING THIS PART'''

== MR Suite Supplies ==
=== Where to order supplies ===
*'''GSR electrodes''' (EL509, 100 electrodes/box): [http://www.biopac.com/disposable-radiotranslucent-dry-electrode Biopac Systems, Inc.]
*'''Self-adhesive wrap''' (Coban tan wrap, item # 2082, 2 in x 5 yardm 36 rolls/box): [http://www.vitalitymedical.com/coban-self-adherent-wrap.html Vitality Medical]

X2go

2021-11-24T20:00:31Z

Jpdiaz: /* OS X */ add info about indirect glx, xquartz, and desktop envs

X2Go provides a desktop GUI for users connecting to a Linux server

===Download x2go Client===

Download X2Go client at:

:https://wiki.x2go.org/doku.php/doc:installation:x2goclient.

====OS X====
*For Mac OS X users, X2Go might get blocked since it's a third-party application. Go to "Security & Privacy" in your Mac to allow open X2Go client.
*Also, XQuartz is required by X2Go. Additional information can be found [https://www.hoffman2.idre.ucla.edu/access/x11_forwarding/#Notes_for_XQuartz_users here].
:Note: From XQuartz 2.7.9, indirect GLX is disabled by default, so you'll need to run this command followed by a reboot:
defaults write org.macosforge.xquartz.X11 enable_iglx -bool true

*To enable a true full-screen view in x2go,
:*Open ''XQuartz'' > ''Preferences'' > and enable ''Full-screen mode''.
*To make ⌘+V work normally, issue the following command in terminal:
 echo "*VT100.translations: #override Meta <KeyPress> V: insert-selection(PRIMARY, CUT_BUFFER0) \n" > ~/.Xdefaults

===Connect===

To setup new sessions for hoffman2, open X2Go client and input either of the following into the "Host" form.

* x2go1.hoffman2.idre.ucla.edu

* x2go2.hoffman2.idre.ucla.edu

[[File:X2go.png | 500px]]

Users can set up multiple sessions connection to different servers with X2Go client.

To Add new sessions, click this [[File:X2go_edit_icon.png | 20px]] icon on the top bar. Then a window pops up as "Session Management".

[[File:X2go_new_session.png | 600px ]]

After login, the desktop Window of your Hoffman2 environment will look like this:

[[File:X2go_desk_top.png | 600px]]

Read more on [https://www.hoffman2.idre.ucla.edu/x2go/ IDRE website]

====Desktop Environment Compatibility====
The following desktop environments (session type) seem to be compatible with Hoffman:
:KDE
:MATE
:XFCE

If you run into issues using KDE, switch to MATE or XFCE since they are considered lightweight GUIs (use less memory and CPU).

'''CentOS7 UPDATE:'''
GNOME and UNITY are not supported at this time and may show a black screen after the connection starts.

For KDE, if fullscreen mode is switched on by default which prevents the menu bar on the bottom to show up, try to delete the following folders before reconnecting to X2Go:
~/.x2go
~/.x2goclient
from your laptop/desktop (in MacOS)
~/.x2go
~/.kde
from your Hoffman2 home directory.

===Known issues===

When using additional commands in ~/.bashrc or ~/.bash_profile, X2Go mistakes the output from certain commands as error messages and will crash or hang when starting a new connection.

====module load====
When using "module load" to load modules in ''~/.bashrc'' or ''~/.bash_profile'', the output from "module load" can be misinterpreted as an error.

Solution:

For example with fsl module, edit your "module load" command in your .bashrc or .bash_profile as following

module load fsl > /dev/null 2>&1

This will redirect the output from "module load" to /dev/null

====fix_perms.sh====
When using [[Hoffman2:Scripts:fix_perms.sh|fix_perms.sh]] or other commands to resolve permission issues when starting new shells, X2Go can freeze due to any "permission denied" messages that occur.

Solution:

: Place fix_perms.sh or any other commands in ''~/.bash_logout''

Commands in ''~/.bash_logout'' are issued when a bash login shell exits. This should resolve issues with X2Go and also allow users to continue using these commands.

Hoffman2:MATLAB

2021-11-11T19:07:21Z

Jpdiaz: /* Software Versions */ update matlab versions available after centos7 upgrade

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program, and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
# Request an interactive node with time and memory required. In this case, 10 hours and 4GB RAM

$ qrsh -l h_rt=10:00:00,h_data=4G

# Load the module MATLAB
$ module load matlab

# You can also load different versions of MATLAB:
# module load matlab/8.6
# or
# module load matlab/R2020b
# Try using "module help" for more information

# Launch MATLAB
$ matlab
</pre>

'''***Please note, launching the Matlab GUI requires ~15-20GB of virtual memory.
<br>Memory can be allocated by requesting the appropriate amount for a single node <code>h_data=20G</code>
or requesting it across several processors <code>h_data=4G -pe shared 5</code> (total 5 * 4G = 20GB memory).
<br>If the GUI is not necessary for running your scripts, then consider launching matlab via text-based interface by issuing the command <code>matlab -nojvm -nodisplay -nosplash</code>.

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7.
Please copy the sample file "myparpooltest_batch.m" first from the path shown below in Hoffman.
* Make sure to not run the myparpooltest_batch.m in MATLAB

1) Request an interactive session with for example:
#* $qrsh -l h_data=4G -pe shared 2

2) When the interactive session is awarded issue:
#* $module load matlab/9.7
#* $matlab &

3) When the matlab desktop opens, issue at the matlab command prompt:
>> rehash toolboxcache
>> configCluster

4) Close matlab

5) To familiarize with the submission procedure you could copy the content of the directory:
#* $cp /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/* ./

7) In a local test directory and issue:
#* $./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f ./myparpooltest_batch.m
(Path: /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/myparpooltest_batch.m)

8) Look into the file:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

9) and/or issues:
#* ./matlab_batch_parallel_job_submit.sh --help

For additional information about MATLAB batch submissions using either a remote or local client, visit the [https://www.hoffman2.idre.ucla.edu/Using-H2/Software/Software.html#matlab MATLAB on Hoffman2] page.

For older versions of Matlab, the [https://www.fieldtriptoolbox.org/faq/how_to_get_started_with_distributed_computing_using_qsub/ Fieldtrip qsub toolbox] can be used to facilitate batch submissions. Please see [[Hoffman2:MATLAB:qsubjobarray.m | qsubjobarray.m]] for an example.

==Software Versions==
The current default version of MATLAB on Hoffman2 is R2020a, but other versions are also available for use:

R2015b or matlab/8.6
R2020b or matlab/R2020b

==External Links==
*[https://www.hoffman2.idre.ucla.edu/Using-H2/Software/Software.html#matlab MATLAB on Hoffman2]

Hoffman2:Accessing the Cluster

2021-11-11T18:56:40Z

Jpdiaz: /* GUI-Enabled SSH */

[[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====
Macs (post - Snow Leopard 10.6.x) no longer come with an X Window System Server pre-installed.

'''Before doing the following steps, please install [http://xquartz.macosforge.org/ XQuartz] and restart your computer.'''
Note: From Xquartz 2.7.9, indirect GLX is disabled by default, so you'll need to run this command followed by a reboot
defaults write org.macosforge.xquartz.X11 enable_iglx -bool true

# Open up your Terminal. It's under ''Applications > Utilities'' on Macs.
# Type the command
#: <pre>$ ssh -Y login_id@hoffman2.idre.ucla.edu</pre>
#: replacing login_id with your Hoffman2 username.
#: The <code>-Y</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 [https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html here] and follow the instructions under ''Windows''. We recommend PuTTY or Cgywin.
#: If you use putty, please install [http://sourceforge.net/projects/xming/ xming] for GUI access.
# Once you have that setup, the process is the same as if you were on a Mac or Linux/Unix machine

==Remote Desktop [Recommended]==
Currently, Hoffman supports connecting to the cluster via the '''X2Go''' client and the '''NoMachine''' client.

===NX Client - GUI===


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).


===X2Go - GUI===
X2Go provides a desktop-like GUI for accessing the Hoffman server. Please see [https://www.ccn.ucla.edu/wiki/index.php/X2go here] to find out more about setup details.





== 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==
*[https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html Hoffman2 Access]
*[[Hoffman2:Accessing_the_Cluster-Historical_Notes | Historical Notes]]

Psychophysics

2021-09-26T23:25:07Z

Jpdiaz: add additional software

==MATLAB==
*[http://psychtoolbox.org/ Psychophysics Toolbox Version 3 (PTB-3)]

==Python==
*[https://www.psychopy.org/ PsychoPy]
*[https://osdoc.cogsci.nl/ OpenSesame]

==JavaScript==
*[https://www.jspsych.org/ jsPsych]
*[https://lab.js.org/ lab.js]
*OSWeb/OpenSesame
*[https://www.psytoolkit.org/ PsyToolkit]

==Web-Based Experiments==
*[https://pavlovia.org/ Pavlovia]
*[https://www.jatos.org/ JATOS]
*[https://gorilla.sc/ GORILLA]

==Other==
*E-Prime
*Presentation
*Experiment Builder (SR Research)

StaglinCenter:EEG

2021-09-26T23:18:41Z

Jpdiaz: /* EEG Facilities & Equipment */ add info about bio-semi eeg suite

This page will give you general information about the EEG Suite including how to use the testing rooms, EGI net information, current EEG projects, and where to locate and order supplies.

==EEG Facilities & Equipment==
The Staglin EEG Suite is part of the [http://www.semel.ucla.edu/staglin Staglin IMHRO Center for Cognitive Neuroscience] and contains resources including two fully shielded EEG suites and a prep room.

The Left EEG Suite:
*[https://www.egi.com/images/stories/manuals/GES_300/GES_300_tman_8103003-51_20150304_hires.pdf EGI Net Amps 300]
*[https://www.egi.com/images/stories/placards/legacy/PIB_instructions_plac_8404162-51_20100427.pdf Polygraph Input Box (PIB) for Net Amps 300]
*[https://www.egi.com/images/stories/company/documents/net_amps_400_flyer_oct_2015_MM_421.pdf MR-safe EGI Net Amps 400]
*[https://www.egi.com/research-division/geodesic-sensor-net EGI HydroCel EEG Nets] - S/M/L of MR and non-MR compatible versions

The Right EEG Suite:
*Bio-Semi 64 channel EEG system using active electrodes

==Using the EEG Suite==
This page describes step-by-step how to schedule, set-up, and test in the Staglin EEG Suite:
*[[StaglinCenter:EEG:Testing]]

'''We recommend giving these directions a complete once-over before you ever take data here.'''

==Troubleshooting and Denoising==
*[[Checking Ground]]
*[[Checking for Wire Loops]]
*[[Checking Scanner Settings]]
*[[Checking Cap Electrodes for Noise]]

==EGI Net Maintenance==
*[https://www.egi.com/images/stories/manuals/Printed%20IFUs%20with%20New%20Notified%20Body/HC_GSN_RM_sponged_appl_uins_8403481-53_20181210.pdf Procedure for Routine Net Tests]
*[https://docs.google.com/forms/d/1qYeNEjPSWKaGmElK9eYHlLOpIOF6R5L1tYh1l861R4E/viewform EGI Net Check-Up Form]
*[https://docs.google.com/spreadsheets/d/1Gx4vqWxGfCX9JPs5AoBQcIU4OveudAx9vv4XIcNJ8YQ/edit#gid=332429759 EGI Net Check-Up Log]

==EEG Suite supplies==
*[[Where to find EEG supplies]]
*[[Where to order EEG supplies]]


==Current Projects==
===Concurrent EEG/fMRI===
*[[SWM Concurrent]]

==Related Info==
===EKG===
If you want to take EKG data concurrently...
*[[StaglinCenter:EEG:EKG]]

==External Links==
*[http://www.egi.com EGI]
*[https://www.egi.com/research-division/net-amps-eeg-amplifier EGI Amp]
*[https://www.egi.com/images/stories/manuals/GES_400/core/GES_400MR_uman_8100401-55_20150722_hires.pdf EGI MR Safe Amp]
*[https://www.egi.com/knowledge-center EGI Knowledge Center]

X2go

2021-09-26T21:42:40Z

Jpdiaz: /* Desktop Environment Compatibility */ update info about centos7 desktop env

x2go provides a desktop GUI for users connecting to a Linux server

===Download x2go Client===

Download x2go client at:

:https://wiki.x2go.org/doku.php/doc:installation:x2goclient.

====OS X====
*For Mac OS X users, x2go might get blocked since it's a third-party application. Go to "Security & Privacy" in your Mac to allow open x2go client.
*Also, XQuartz is required by x2go. Additional information can be found [https://www.hoffman2.idre.ucla.edu/access/x11_forwarding/#Notes_for_XQuartz_users here].
*To enable a true full-screen view in x2go,
:*Open ''XQuartz'' > ''Preferences'' > and enable ''Full-screen mode''.
*To make ⌘+V work normally, issue the following command in terminal:
 echo "*VT100.translations: #override Meta <KeyPress> V: insert-selection(PRIMARY, CUT_BUFFER0) \n" > ~/.Xdefaults

===Connect===

To setup new sessions for hoffman2, open x2go client and input either of the following into the "Host" form.

* x2go1.hoffman2.idre.ucla.edu

* x2go2.hoffman2.idre.ucla.edu

[[File:X2go.png | 500px]]

Users can setup multiple sessions connection to different servers with x2go client.

To Add new sessions, click this [[File:X2go_edit_icon.png | 20px]] icon on the top bar. Then a window pops up as "Session Management".

[[File:X2go_new_session.png | 600px ]]

After login, the desktop Window of your Hoffman2 environment will look like this:

[[File:X2go_desk_top.png | 600px]]

Read more on [https://www.hoffman2.idre.ucla.edu/x2go/ idre website]

====Desktop Environment Compatibility====
The following desktop environments (session type) seem to be compatible with Hoffman:
:KDE
:MATE

'''CentOS7 UPDATE:'''
GNOME and UNITY are not supported at this time and may show a black screen after the connection starts.

For KDE, if fullscreen mode is switched on by default which prevents the menu bar on the bottom to show up, try to delete the following folders before reconnecting to x2go:
~/.x2go
~/.x2goclient
from your laptop/desktop (in MacOS)
~/.x2go
~/.kde
from your Hoffman2 home directory.

===Known issues===
When using additional commands in ~/.bashrc or ~/.bash_profile, X2Go mistakes the output from certain commands as error messages and will crash or hang when starting a new connection.

====module load====
When using "module load" to load modules in ''~/.bashrc'' or ''~/.bash_profile'', the output from "module load" can be misinterpreted as an error.

Solution:

For example with fsl module, edit your "module load" command in your .bashrc or .bash_profile as following

module load fsl > /dev/null 2>&1

This will redirect the output from "module load" to /dev/null

====fix_perms.sh====
When using [[Hoffman2:Scripts:fix_perms.sh|fix_perms.sh]] or other commands to resolve permission issues when starting new shells, X2Go can freeze due to any "permission denied" messages that occur.

Solution:

: Place fix_perms.sh or any other commands in ''~/.bash_logout''

Commands in ''~/.bash_logout'' are issued when a bash login shell exits. This should resolve issues with X2Go and also allow users to continue using these commands.

Main Page

2021-06-22T00:27:10Z

Jpdiaz: /* Center for Cognitive Neuroscience at UCLA */ create new page. comment out pages under construction

__NOTOC__
== Center for Cognitive Neuroscience at UCLA ==

Welcome to the Wiki of the Center for Cognitive Neuroscience at UCLA (CCN at UCLA). Please find and contribute helpful information for lab usage here.

=== Classes ===
* [[CCN Workshops]]
* [[Neuroimaging+ Journal Club]]
* [[Principles of Neuroimaging - 2016-2017]]
* [[Principles of Neuroimaging - 2015-2016]]

=== Computing ===
* [[Hoffman2]]
* [[Dicom]]
* [[Psychophysics]]


=== EEG/fMRI ===
* [[EEG]] (includes EEG-fMRI)
* [[MR]]


=== Staglin Center ===
* [[Staglin EEG Suite]]
* [[Staglin MR Suite]]

Resources at UCLA

2021-06-22T00:19:52Z

Jpdiaz: create resources page

== '''UNDER CONSTRUCTION:''' Resources for Students, Staff, & Faculty at UCLA ==

Below is a list of resources available for UCLA members.

=== Google Apps for UCLA ===
* https://g.ucla.edu/

=== Office 365 ===
* Microsoft Office ProPlus (Students)

=== Box ===
* https://ucla.account.box.com/
* https://uclahs.account.box.com/

=== MATLAB ===
* Academic Licenses
* https://softwarecentral.ucla.edu/matlab-getmatlab
* https://www.mathworks.com/academia/tah-portal/ucla-31454052.html

=== Collaboration Tools ===
* '''Slack'''
** ucla.slack.com

* '''Zoom'''
** https://ucla.zoom.us/
** https://ucla-hipaa.zoom.us

=== Security Software ===
* '''Sophos Anti-Virus'''
** Available at NO COST through October of 2021.
** https://www.it.ucla.edu/it-support-center/software-downloads/sophos-antivirus

* '''FrontDoorSoftware'''
** Available for up to four years
** https://frontdoorsoftware.com/UCLA/

=== References ===
* https://softwarecentral.ucla.edu/
* https://www.it.ucla.edu/it-support-center
* https://www.it.ucla.edu/connect-at-home

EEG

2021-06-15T01:02:42Z

Jpdiaz: /* ICA */ create AMICA page

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.
*[[General Pre-Processing Steps]]

===Programs for EEG data processing===
Standalone Applications
*[[Netstation]]
*[[BrainVision Analyzer]]
MATLAB Toolboxes
*[https://sccn.ucsd.edu/eeglab/index.php EEGLAB]
*[https://www.fieldtriptoolbox.org/ FieldTrip]
*[https://neuroimage.usc.edu/brainstorm/ Brainstorm]
Python Packages
*[https://mne.tools/stable/index.html MNE]

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

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

*[[Under Construction]]

== Support ==
*[[EGI]]
*[[ICLabel]]

== History ==

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

EEG

2021-06-06T01:20:36Z

Jpdiaz: /* Programs for EEG data processing */ add brainstorm

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.
*[[General Pre-Processing Steps]]

===Programs for EEG data processing===
Standalone Applications
*[[Netstation]]
*[[BrainVision Analyzer]]
MATLAB Toolboxes
*[https://sccn.ucsd.edu/eeglab/index.php EEGLAB]
*[https://www.fieldtriptoolbox.org/ FieldTrip]
*[https://neuroimage.usc.edu/brainstorm/ Brainstorm]
Python Packages
*[https://mne.tools/stable/index.html MNE]

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

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

*[[Under Construction]]

== Support ==
*[[EGI]]
*[[ICLabel]]

== History ==

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

ICLabel

2021-05-04T04:05:32Z

Jpdiaz: add information about compiling MatConvNet for ICLabel on Hoffman

==How to properly install ICLabel on Hoffman==
After downloading ICLabel and placing it in the eeglab plugins folder, MatConvNet should be compiled for optimal CPU computations.

First, request an interactive session, then load the required software:
# load env
module load gcc/4.9.3 # 4.8 or newer
module load matlab/9.1 # R2015b or newer

# open matlab
matlab &

Once Matlab is open, change the directory to the MatConvNet folder and compile the library using the following:
% compile matconvnet
cd eeglab/plugins/ICLabel1.2.6/matconvnet
addpath matlab

% configure mex to use 'g++'
mex -setup C++
vl_compilenn('verbose', 1)

% test library
vl_testnn

===Resources===
*[https://labeling.ucsd.edu/tutorial ICLabel]
*[https://www.vlfeat.org/matconvnet/install/ MatConvNet]

EEG

2021-05-04T03:44:39Z

Jpdiaz: /* Support */ create page for ICLabel install support

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.
*[[General Pre-Processing Steps]]

===Programs for EEG data processing===
Standalone Applications
*[[Netstation]]
*[[BrainVision Analyzer]]
MATLAB Toolboxes
*[https://sccn.ucsd.edu/eeglab/index.php EEGLAB]
*[https://www.fieldtriptoolbox.org/ FieldTrip]
Python Packages
*[https://mne.tools/stable/index.html MNE]

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

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

*[[Under Construction]]

== Support ==
*[[EGI]]
*[[ICLabel]]

== History ==

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

Hoffman2:MATLAB:qsubjobarray.m

2021-04-01T09:16:16Z

Jpdiaz: remove reference to amica to provide separate details about running amica via openmpi on hoffman

%% qsubjobarray.m
%
% This script uses the Fieldtrip qsub toolbox to submit a job array
% that runs the function 'step2_preprocessUpToDipfit' on each individual .set file.
%

% add paths, which will be passed to qsub
addpath /u/project/CCN/apps/matlab/fieldtrip/qsub/ % qsub toolbox
addpath /u/project/CCN/apps/matlab/eeglab/14.1.0b/ % eeglab

% generate list of all .set files within specific folder
FILELIST=dir('/u/project/labgroup/EEG/allsubjs/reprocessed/step1/*.set');

% commands to setup env
qmem = 2024*2024*2024; % in bytes (~8GB)
qtim = 14400; % in seconds (4HR)
qopt = '-j y -pe shared 4 '; % options (note trailing space)

% usual commands to initiate matlab
matlabcmd='. /u/local/Modules/default/init/modules.sh; module load matlab/9.1; matlab';

%% Submit Job Array
jobidarray={};

% Enter the main loop
for i = 1:size(FILELIST,1) % 500 per user job limit

% call to qsubfeval command
jobidarray{i}= qsubfeval(@step2_preprocessUpToDipfit, FILELIST(i), ...
'memreq', qmem, ... % bytes
'timreq', qtim, ... % seconds
'backend', 'sge', ... % SGE
'diary', 'always', ... % log level
'options', qopt, ...
'matlabcmd', matlabcmd);

pause(10) % 10 seconds (to avoid overload)

end

% save array to load output at later time
save jobarray.mat jobidarray

Hoffman2:MATLAB:qsubjobarray.m

2021-03-30T00:40:46Z

Jpdiaz: fieldtrip qsub example

%% qsubjobarray.m
%
% This script uses the Fieldtrip qsub toolbox to submit a job array
% that runs the function 'step2_preprocessUpToDipfit' on each individual .set file.
% The function performs ASR, AMICA, DIPFIT, and ICLabel which can take about
% 3000-14000 seconds to run on a single subject.
%

% add paths, which will be passed to qsub
addpath /u/project/CCN/apps/matlab/fieldtrip/qsub/ % qsub toolbox
addpath /u/project/CCN/apps/matlab/eeglab/14.1.0b/ % eeglab

% generate list of all .set files within specific folder
FILELIST=dir('/u/project/labgroup/EEG/allsubjs/reprocessed/step1/*.set');

% commands to setup env
qmem = 2024*2024*2024; % in bytes (~8GB)
qtim = 14400; % in seconds (4HR)
qopt = '-j y -pe shared 4 '; % options (note trailing space)

% usual commands to initiate matlab
matlabcmd='. /u/local/Modules/default/init/modules.sh; module load matlab/9.1; matlab';

%% Submit Job Array
jobidarray={};

% Enter the main loop
for i = 1:size(FILELIST,1) % 500 per user job limit

% call to qsubfeval command
jobidarray{i}= qsubfeval(@step2_preprocessUpToDipfit, FILELIST(i), ...
'memreq', qmem, ... % bytes
'timreq', qtim, ... % seconds
'backend', 'sge', ... % SGE
'diary', 'always', ... % log level
'options', qopt, ...
'matlabcmd', matlabcmd);

pause(10) % 10 seconds (to avoid overload)

end

% save array to load output at later time
save jobarray.mat jobidarray

MR

2021-03-26T01:55:01Z

Jpdiaz: /* Processing */ link to software page

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.
*[[Staglin MR Suite]]

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



==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]]

===Additional Tools===
*[https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Software_Tools Software on Hoffman2]

Hoffman2:MATLAB

2021-03-26T01:41:49Z

Jpdiaz: /* Software Versions */ update and add information about fieldtrip qsub toolbox

[[Hoffman2|Back to all things Hoffman2]]

MATLAB is not a small program, and it can handle some fairly complex graphics. As such, this is not something suitable to be used on a login node of Hoffman2. But that's already been thought of by the great people at ATS.

==GUI==
To run a full GUI session of MATLAB, execute
$ matlab
That's it, no flags, no frills, nothing else. Hoffman2 will automatically check out an appropriate interactive node for you to run MATLAB on. All you have to do is provide a time limit (in hours) when they ask you
Enter a time limit for your session in hours (default 2)
<or quit>:

==Command Line==
If you don't need the fancy GUI and want the command line, execute
$ matlab -nodesktop
and then supply a time limit when asked.

'''Since this uses interactive nodes, the maximum time limit you can request is 24 hours.'''

==License Check==
With so many people using Hoffman2 and MATLAB, sometimes licenses run out. Using this helpful script will give you some insight as to the license situation.

[[Hoffman2:Scripts:matlab_license_check.sh|matlab_license_check.sh]]

==Large Computations==
If you are doing a larger computation, '''running MATLAB normally will probably not work well.'''

Using the default method of launching MATLAB on Hoffman2 checks out an [[Hoffman2:Interactive_Sessions | interactive node]] with only 1GB of RAM. This is woefully small if you are working with ten minutes of dense array EEG. Use the following steps to launch a more capable MATLAB session.

<pre>
# Request an interactive node with time and memory required. In this case, 10 hours and 4GB RAM
$ qrsh -l i,h_rt=10:00:00,h_data=4G

# Load the module MATLAB
$ module load matlab

# You can also load different versions of MATLAB:
# module load matlab/7.14
# or
# module load matlab/8.1
# Try using "module help" for more information

# Launch MATLAB
$ matlab
</pre>

'''***Please note, launching the Matlab GUI requires ~15-20GB of virtual memory.
<br>Memory can be allocated by requesting the appropriate amount for a single node <code>h_data=20G</code>
or requesting it across several processors <code>h_data=4G -pe shared 5</code> (total 5 * 4G = 20GB memory).
<br>If the GUI is not necessary for running your scripts, then consider launching matlab via text-based interface by issuing the command <code>matlab -nojvm -nodisplay -nosplash</code>.

==Running Parallel Jobs==
IDRE team provided the following solution to use parallel pool in Matlab version 9.7.
Please create the [[Hoffman2:parpoolexample.m | parpoolexample.m]] first, where you initiate a pool with the number of workers needed to run the job.
* Make sure to not run the papoolexample.m in MATLAB

1) Request an interactive session with for example:
#* $qrsh -l h_data=4G -pe shared 1

2) When the interactive session is awarded issue:
#* $module load matlab/9.7
#* $matlab &

3) When the matlab desktop opens, issue at the matlab command prompt:
>> rehash toolboxcache
>> configCluster

4) Close matlab

5) To familiarize with the submission procedure you could copy the content of the directory:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION

7) In a local test directory and issue:
#* ./matlab_batch_parallel_job_submit.sh -t 3 -s 20 -m 4 -v 9.7 -f [[Hoffman2:parpoolexample.m | parpoolexample.m]]

8) Look into the file:
#* /u/local/apps/submit_scripts/MATLAB_PARALLEL_BATCH_SUBMISSION/README.HOWTO

9) and/or issues:
#* ./matlab_batch_parallel_job_submit.sh --help

For additional information about MATLAB batch submissions using either a remote or local client, visit the [https://www.hoffman2.idre.ucla.edu/Using-H2/Software/Software.html#matlab MATLAB on Hoffman2] page.

For older versions of Matlab, the [https://www.fieldtriptoolbox.org/faq/how_to_get_started_with_distributed_computing_using_qsub/ Fieldtrip qsub toolbox] can be used to facilitate batch submissions. Please see [[Hoffman2:MATLAB:qsubjobarray.m | qsubjobarray.m]] for an example.

==Software Versions==
The current default version of MATLAB on Hoffman2 is R2015b, but more recent versions are also available for use:

R2016b or matlab/9.1
R2019b or matlab/9.7
R2020a or matlab/9.8

==External Links==
*[https://www.hoffman2.idre.ucla.edu/Using-H2/Software/Software.html#matlab MATLAB on Hoffman2]

WSL

2021-03-25T20:44:09Z

Jpdiaz: /* Windows Subsystem for Linux */ instructions for wsl

=Windows Subsystem for Linux=

==Installation==
To download Windows Subsystem for Linux, follow the [https://docs.microsoft.com/en-us/windows/wsl/install-win10 instructions] provided by Microsoft.
The rest of these instructions will assume that Ubuntu 20.04 LTS was chosen for installation.

==GUI apps==
To open GUI apps from WSL, you will need a Windows X Server running under Windows. A free one can be downloaded from [https://sourceforge.net/projects/vcxsrv/ here].

Display may also need to be setup. Run a quick test by issuing this command in terminal:

echo $DISPLAY

An IP address should be printed. If nothing appears, then follow the instructions below to set it up (under "export appropriate display variables"):

https://skeptric.com/wsl2-xserver/

It also goes over how to setup your firewall for the apps.

==Neurodebian==
To download neuroscience-related software tools, the NeuroDebian repository can be added to the package manager (specify OS, server location, and whichever software component you want, then follow the instructions): https://neuro.debian.net/

After this repository is added, you should be able to download any software tool they provide. For example, to download mricron, issue the following command:

sudo apt update
sudo apt install mricron

Once it's been installed, you can test the app by opening the Xserver on windows then typing the command mricron in your Linux terminal. The app should then open as a separate window.

To mount Hoffman from WSL, follow the instructions [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Sharing_Filesystems here].

Hoffman2:Software Tools

2021-03-22T20:40:04Z

Jpdiaz: update list of software versions

WSL

2021-02-23T21:02:36Z

Jpdiaz: WSL page creation

=Windows Subsystem for Linux=

Psychophysics

2021-02-04T00:24:41Z

Jpdiaz: resources added

MR:DirectoryStructure

2021-02-04T00:00:20Z

Jpdiaz: add data structure resources

Standards are great because they let people from different places and backgrounds view the same thing and understand the same basic information. Traffic lights are standardized within jurisdictions so all the drivers there understand them. Directory structures for MR data are standardized here so that all the members of the lab can understand the data and collaborate on it together. Below we detail this standardization.

==Root Directory==
On [[Hoffman2]], within the directory:
/u/project/
each PI will have their own project space under their username.

...

==Resources==
*[https://bids-specification.readthedocs.io/en/latest/ Brain Imaging Data Structure (BIDS)]

EEG:DirectoryStructure

2021-02-03T23:59:32Z

Jpdiaz: add data structure resources

==Resources==
*[https://bids-specification.readthedocs.io/en/latest/ Brain Imaging Data Structure (BIDS)]
*[https://doi.org/10.1038/s41597-019-0104-8 EEG-BIDS]

Hoffman2:Sharing Filesystems

2021-02-03T23:46:14Z

Jpdiaz: /* Installation */ add install instructions for linux systems

[[Hoffman2|Back to all things Hoffman2]]

There are apps for linking filesystems so that you can access data across machines. It's like mounting a shared drive. Here we present a [[Hoffman2:Sharing Filesystems#MacFusion|GUI]] and a [[Hoffman2:Sharing Filesystems#sshfs|command line]] way of accomplishing this.

==MacFusion==
MacFusion is no longer working as of macOS 10.12 (Sierra). Please use the [[Hoffman2:Sharing Filesystems#sshfs|command line]] instructions below.


==sshfs==


===Installation===

====macOS====
Download and install the two packages on this website: https://osxfuse.github.io/
* FUSE for macOS
* SSHFS

====Linux====
Red Hat
yum install sshfs

Debian
apt install sshfs

===Usage===
Let's say you want to mount Hoffman2 locally. In your Mac terminal, using the command line, execute:
$ id
uid=1010(joebruinuser) gid=20(bruingroup1),23(bruingroup2),...
$ mkdir ~/MOUNTPOINT
$ sshfs -o idmap=user -o uid=1010 -o gid=20 USERNAME@hoffman2.idre.ucla.edu:/path/to/mount ~/MOUNTPOINT
Where,
; <code>id</code>
: Gets information about your local user, including your numerical ID and group ID(s)
; <code>-o idmap=user -o uid=1010 -o gid=20</code>
: Translates your local user and group IDs to that of the remote user so you can read and write files as if you were on the remote machine. Make sure to put the correct user and group IDs that were returned by the <code>id</code> command.
; <code>USERNAME</code>
: Is your username at the remote computer.
; <code>hoffman2.idre.ucla.edu</code>
: Is the address of the remote computer you are connecting to.
; <code>/path/to/mount</code>
: Could be left blank to mount your home directory from the remote computer, or it could specify any point in the remote filesystem.
; <code>MOUNTPOINT</code>
: Is the name of the directory where the remote filesystem will be mounted.

To unmount:
* Use the command
umount ~/MOUNTPOINT
or
* Right click on the desktop icon that appears and select ''"Eject."''

===Permission Error===
SSHFS has two permission checks, one performed by the macOS and one performed by the remote filesystem. In certain cases, the remote host will allow access to the directory but the macOS encounters issues translating the filesystem permissions. This will result in a permission denied error.

If you run into this permission denied error:
* Double check that you are using the correct user and group IDs that were returned by the <code>id</code> command.
* Include the option <code>defer_permissions</code>.
Where,
; <code>-o defer_permissions</code>
: Disables local permission checks and defers all permission requests to the remote server.

StaglinCenter:EEG

2020-11-11T00:56:30Z

Jpdiaz: /* EEG Suite supplies */ remove not so current list of supplies & organize to match MR Suite page

This page will give you general information about the EEG Suite including how to use the testing rooms, EGI net information, current EEG projects, and where to locate and order supplies.

==EEG Facilities & Equipment==
The Staglin EEG Suite is part of the [http://www.semel.ucla.edu/staglin Staglin IMHRO Center for Cognitive Neuroscience] and contains resources including:
*[https://www.egi.com/images/stories/manuals/GES_300/GES_300_tman_8103003-51_20150304_hires.pdf EGI Net Amps 300]
*[https://www.egi.com/images/stories/placards/legacy/PIB_instructions_plac_8404162-51_20100427.pdf Polygraph Input Box (PIB) for Net Amps 300]
*[https://www.egi.com/images/stories/company/documents/net_amps_400_flyer_oct_2015_MM_421.pdf MR-safe EGI Net Amps 400]
*[https://www.egi.com/research-division/geodesic-sensor-net EGI HydroCel EEG Nets] - S/M/L of MR and non-MR compatible versions

==Using the EEG Suite==
This page describes step-by-step how to schedule, set-up, and test in the Staglin EEG Suite:
*[[StaglinCenter:EEG:Testing]]

'''We recommend giving these directions a complete once-over before you ever take data here.'''

==Troubleshooting and Denoising==
*[[Checking Ground]]
*[[Checking for Wire Loops]]
*[[Checking Scanner Settings]]
*[[Checking Cap Electrodes for Noise]]

==EGI Net Maintenance==
*[https://www.egi.com/images/stories/manuals/Printed%20IFUs%20with%20New%20Notified%20Body/HC_GSN_RM_sponged_appl_uins_8403481-53_20181210.pdf Procedure for Routine Net Tests]
*[https://docs.google.com/forms/d/1qYeNEjPSWKaGmElK9eYHlLOpIOF6R5L1tYh1l861R4E/viewform EGI Net Check-Up Form]
*[https://docs.google.com/spreadsheets/d/1Gx4vqWxGfCX9JPs5AoBQcIU4OveudAx9vv4XIcNJ8YQ/edit#gid=332429759 EGI Net Check-Up Log]

==EEG Suite supplies==
*[[Where to find EEG supplies]]
*[[Where to order EEG supplies]]


==Current Projects==
===Concurrent EEG/fMRI===
*[[SWM Concurrent]]

==Related Info==
===EKG===
If you want to take EKG data concurrently...
*[[StaglinCenter:EEG:EKG]]

==External Links==
*[http://www.egi.com EGI]
*[https://www.egi.com/research-division/net-amps-eeg-amplifier EGI Amp]
*[https://www.egi.com/images/stories/manuals/GES_400/core/GES_400MR_uman_8100401-55_20150722_hires.pdf EGI MR Safe Amp]
*[https://www.egi.com/knowledge-center EGI Knowledge Center]

Staglin MR Suite

2020-11-11T00:50:11Z

Jpdiaz: /* MRI Facilities & Equipment */ add info about dedicated iMac and multimodal data collection

==MRI Facilities & Equipment==

===Scanning Facilities===
The Staglin IMHRO Center for Cognitive Neuroscience operates a Siemens 3 Tesla Prisma Fit MRI Scanner equipped with 20, 32, and 64 channel head coils.

===Peripheral Equipement===
Peripheral equipment available for projects include:
*Siemens headphone/speak system,
*Siemens physiological measurement system,
**Includes pulse, respiration, and EKG.
*[http://www.mrivideo.com/visuastimdigital.php VisuaStim digital system] by Resonance Technology Corporation (RTC),
**Includes goggles/headphone/controller unit.
*[http://www.optoacoustics.com/medical/optoactive-ii Optoacoustics] noise-canceling headphones and microphone,
*Avotech mini projector system,
**LCD projection system controlled via fiberoptic cabling.
*4-button and 2-button response pads by Current Designs,
*32 channel electronic interface and power supply unit, and
*BioPac MP150 for collecting physiological measures.
**Includes skin conductance, respiration rate, and pulse rate/waveform.

===Multimodal Data Collection===
*[https://www.ccn.ucla.edu/wiki/index.php/StaglinCenter:EEG-FMRI Concurrent EEG]
*[[Low Frequency Focused Ultrasound]]
*[[Eye Tracking]]

===Dedicated iMac Computer===
The MR suite is equipped with a dedicated iMac computer with a dual-boot Windows partition, currently running:
*Psychophysics Software:
**Psychtoolbox,
**PsychoPy,
**E-Prime,
*MATLAB 2015b
*AcqKnowledge 4 (for BioPac MP150)
*[[FIRMM]]

For new software, please contact the MR Technician before installation.

== How to record EKG using the Siemens built-in system ==
The Siemens Trio Scanner comes with its own EKG monitoring system which wirelessly transmits the patient EKG signal to the recording computer.

=== Setting up the EKG ===
The same principles of EKG prep hold true, except there are three leads: Right Arm, Right Leg and Left Leg
# Prepare the areas by wiping them down with an alcohol wipe
# Scrub the areas with a cotton swab using NuPrep
# Re-clean the area with an alcohol wipe and allow to dry
# Apply lead stickers to each of the areas and connect the proper EKG leads to them, they are labeled:
*RA - Right Arm
*RL - Right Leg
*LL - Left Leg
# Tape down the EKG leads so they stay connected to the stickers.
# Tape down the wireless device box so it doesn't move.
# Prep the subject for EEG

=== Setting up the Scanner ===
'''STILL TESTING THIS PART'''

== MR Suite Supplies ==
=== Where to order supplies ===
*'''GSR electrodes''' (EL509, 100 electrodes/box): [http://www.biopac.com/disposable-radiotranslucent-dry-electrode Biopac Systems, Inc.]
*'''Self-adhesive wrap''' (Coban tan wrap, item # 2082, 2 in x 5 yardm 36 rolls/box): [http://www.vitalitymedical.com/coban-self-adherent-wrap.html Vitality Medical]

StaglinCenter:EEG:Net

2020-10-26T07:45:27Z

Jpdiaz: update instructions

All the supplies you will need can be found in/on the wooden cabinet in the prep room. Inside the cabinet, there is a box marked "EEG Prep Supply" which contains smaller items such as the measuring tape, the red pencil, and scissors.

===Preparing the Electrolyte Solution===

:1. In the prep room, grab an empty plastic bucket and fill it with '''warm''' water to the 2 quart line.

:2. Mix in 1 scoop of the potassium chloride and 1 spoonful of shampoo.

::*Each has its own measuring spoon which you should find in the potassium chloride box and next to the shampoo. The spoons are also conveniently named "potassium chloride" and "shampoo" on their handles. You can use the "shampoo" spoon to stir the solution until the ingredients have fully dissolved.

===Fitting the Right Net===

:1. Measure the circumference of the largest part of your subject's head in centimeters (usually sits right above the eyes).

:2. Match this measurement to the range displayed on the plug of one of the nets.

===Measuring and Marking the Vertex===

To find the point where the Cz electrode (REF) should sit, you'll take 2 perpendicular measurements with the red pencil in hand:

:1. Measure from behind the top of one ear to the same point behind the other ear (like where a headband would sit).
::*Draw a short perpendicular line at the midpoint of this distance.

:2. For the perpendicular nasion/inion measurement, ask the subject to hold the starting end of the measuring tape between his or her eyes and then draw the tape back to just below the bump at the back of the head.
::*Draw a short perpendicular line at the midpoint of this distance.

:3. Referencing your 2 marks, draw a cross at the intersection to find the vertex.

===Soaking the Net===

:1. Wrap the towel around the plug of the previously determined net. This connection must always remain '''DRY'''!

:2. Turn the net inside out with the sponges facing out, make sure all clasps are fully loosened, and immerse the net in the electrolyte solution so that all sensors are fully submerged.
::*It is easiest to place the wrapped plug on a chair and then have the bucket of solution on the floor or in the sink to ensure the plug doesn't come near water.

:3. Let the net soak for 5-10 minutes.
::*If the net is soaked for too long, it may take up too much solution which can cause bridging between sensors so be mindful of the time!

===Applying the Net===

:1. Have the subject sit in a chair facing you. Place the bucket with the soaking net on the floor in front of them and ask them to hold the wrapped plug in their lap. Place a towel over his or her shoulders to catch drips.

:2. Turn the net back the right way (sponges in) and gently shake excess electrolyte solution from the net.

:3. Place both hands inside the net with your fingers spread out to stretch the net.
::*The elastics holding the net together are very delicate so careful not to overstretch the net!

:4. Instruct your subject to close his or her eyes.

:5. Begin to bring the stretched net straight down over your subject's head. Align the center front electrode between their eyes and then slightly rotate your hands back to stretch the net back and down the back of the head.

:6. Tighten the sides and then center clasps.
::*At this point you may allow your subject to open his or her eyes and dry any drips as needed.

:7. To align the cap over the earholes correctly and to match REF to the vertex, plant all five fingers in the net and then move as needed, wiggling the net a bit to allow the sensors to find their way through the hair to the scalp.
::*Once again, the net is very delicate! Moving with the whole hand, fingers planted in various positions will more gently and efficiently shift/move the net for you.

===Plugging the Net into the EGI Amplifier===

Plug the net into the amp by first positioning the plug in the amp and then turning the knob from down to up. The cord of the net will be to the RIGHT of the plug. The plug will draw itself into the correct position. '''Do not force the plug into the amp. The pins in the connector are very fragile.'''

===Helpful Tips===
*You will want to bring the bucket of electrolyte solution with you into the testing suite as you will need it to lower impedance ( [[StaglinCenter:EEG:ImpedanceCheck]] ). '''However''', place it under a chair or in a corner where it is far from the equipment on the floor and will not be tripped on and spilled!

*It is also suggested that you leave the towel over your subject's shoulders for the entire task to catch any drips that may occur later on.

===References:===

[https://www.egi.com/images/stories/manuals/Second%20Batch%20of%20IFUs%20with%20new%20Notified%20Body%20Jan%202019/HC_GSN_MR_uins_8402110-01_20181221.pdf EGI Application Instructions]
*The EGI instructions can be found in the black binder in the cabinet in the prep room.

<div style="text-align: center; border: 1px dotted gray;"> Return to [[StaglinCenter:EEG:Testing]]</div>

StaglinCenter:EEG:Testing

2020-10-26T07:35:23Z

Jpdiaz: /* Feedback Form */

==Reserving the EEG Suite==
There is a [https://www.google.com/calendar/embed?src=28vln94hoc2da1k40rn6lcp1bs%40group.calendar.google.com&ctz=America/Los_Angeles Google Calendar] for reserving the Staglin EEG Suite.

Request access to this calendar by emailing Agatha (alenarto@ucla.edu). When you are ready to take EEG data, make a reservation on this calendar ahead of time.

==EEG Collection Setup==

===Testing Setup===
This is an outline of a basic testing setup to do an audio and visual EEG setup in the EEG suite:
*[[EEG Testing Setup]]

If you are working on a current project, please follow the protocol regarding your project by going to the project page:
*[[SWM EEG]]

===Elecrode Digitization===
If you care to use the [https://sccn.ucsd.edu/wiki/Get_chanlocs 3D Structure Sensor] to record the electrode placement on your subject. This is useful for [[EEG:Processing:Source|source localization]].

==EEG Net Prep and Application==
EGI has some how-to's on this, and we recommend you read the manuals (located in the cabinet above the table in the EEG collection room). But we've got a step-by-step here for you.
*[[StaglinCenter:EEG:Net]]

==Collect Data==
===Starting Net Station===
Once the net has been placed on your subject, follow these steps to properly start up Net Station.
*[[StaglinCenter:EEG:StartingNetStation]]

===Checking Impedance===
You need to check the impedance of the electrodes and fix any that are too high or else your data collection will not be ideal.
*[[StaglinCenter:EEG:ImpedanceCheck]]

===Data Storage===
Where to save your data so you are a responsible user and can find it in the future.
*[[StaglinCenter:EEG:Collect]]

===Exporting Data===
After data collection, many decide to export their data onto the Hoffman2 server; however, NetStation files are cumbersome to work with because of their size and format. Therefore, here are some data export instructions to convert and export files in your desired format:
*[[StaglinCenter:EEG:Export]]

==Feedback Form==
For quality control, we devised a feedback form that we ask researchers to fill out each time they collect data in the Staglin EEG Suite. Access to the form is located on the desktop of the Netstation computer, labeled steps 1 and 2:

:1. Step 1 - logs you onto the Internet and pulls up the EEG Feedback Form
:2. Step 2 - disconnects Internet. '''NOTE: This is important to do so the next tester will not be connected to the Internet while testing. Internet connection can disrupt recording'''

The identification names of each net can be found on the plug.



==Clean Up==

===Net Disinfection===
After each use, rinse out and disinfect the net by following this step-by-step process.
*[[StaglinCenter:EEG:Disinfect]]

<div style="text-align: center; border: 1px dotted gray;"> Return to [[Staglin EEG Suite]] home page</div>

Hoffman2:JupyterNotebook

2020-10-26T07:21:34Z

Jpdiaz: /* Method 1: */ fix broken links, restructure content, and add GPU information

=Use Jupyter Notebook/Lab=

==Install on Local Device==
Install to your laptop using Anaconda:

[https://jupyter.readthedocs.io/en/latest/install.html Jupyter Official Website]

#Download [https://www.anaconda.com/distribution/ Anaconda] version 3.7
#Install it to your laptop as a regular application
#then run "jupyter notebook" from the terminal

==Connecting to Hoffman2==
Download h2jupynb from [https://gitlab.idre.ucla.edu/dauria/jupyter-notebook git ] to your local drive

chmod u+x h2jupynb

From your laptop, run (Using Python 3.7)

./h2jupynb -u userid -v 3.7.0

(You'll find more details [https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html#connecting-via-jupyter-notebook-lab here])

===GPU Access===
To access GPU resources on Hoffman, add the virtual env to ipykernel for the very first time:

qrsh -l gpu,P4
module load python/anaconda3
conda activate pytorch-1.3.1-gpu
python -m ipykernel install --user --name=pytorch-1.3.1-gpu

Using h2jupynb:
./h2jupynb -v anaconda3 -g yes -c P4 -l 10.0

Hoffman2:Accessing the Cluster

2020-10-26T06:54:16Z

Jpdiaz: fix broken link

[[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====
Macs (post - Snow Leopard 10.6.x) no longer come with an 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].
***WARNING*** MacOSX10 Yosemite needs to add "export Display=:0.0" to the local user Profile in order for it to work.
# Open up X11/XQuartz or Terminal. Both are under ''Applications > Utilities'' on Macs.
# Type the command
#: <pre>$ ssh -Y login_id@hoffman2.idre.ucla.edu</pre>
#: replacing login_id with your Hoffman2 username.
#: The <code>-Y</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 [https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html here] and follow the instructions under ''Windows''. We recommend PuTTY or Cgywin.
#: If you use putty, please install [http://sourceforge.net/projects/xming/ xming] for GUI access.
# Once you have that setup, the process is the same as if you were on a Mac or Linux/Unix machine

==Remote Desktop [Recommended]==
Currently, Hoffman supports connecting to the cluster via the '''X2Go''' client and the '''NoMachine''' client.

===NX Client - GUI===


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).


===X2Go - GUI===
X2Go provides a desktop-like GUI for accessing the Hoffman server. Please see [https://www.ccn.ucla.edu/wiki/index.php/X2go here] to find out more about setup details.





== 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==
*[https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html Hoffman2 Access]
*[[Hoffman2:Accessing_the_Cluster-Historical_Notes | Historical Notes]]

Main Page

2020-10-23T22:48:31Z

Jpdiaz: /* Computing */ create psychophysics page

__NOTOC__
== Center for Cognitive Neuroscience at UCLA ==

Welcome to the Wiki of the Center for Cognitive Neuroscience at UCLA (CCN at UCLA). Please find and contribute helpful information for lab usage here.

=== Classes ===
* [[Neuroimaging+ Journal Club]]
* [[Principles of Neuroimaging - 2016-2017]]
* [[Principles of Neuroimaging - 2015-2016]]

=== Computing ===
* [[Hoffman2]]
* [[Dicom]]
* [[Psychophysics]]


=== EEG/fMRI ===
* [[EEG]] (includes EEG-fMRI)
* [[MR]]
* [[fNIRS]]

=== Staglin Center ===
* [[Staglin EEG Suite]]
* [[Staglin MR Suite]]

Eye Tracking

2020-10-23T19:44:58Z

Jpdiaz: create eye tracking page

=EyeLink=
==Settings==
[[File:Image-size-projector-screen.png]]

[[File:Eyelink-in-scanner-eye-to-screen-distance.png]]

File:Eyelink-in-scanner-eye-to-screen-distance.png

2020-10-23T19:44:10Z

Jpdiaz:

File:Image-size-projector-screen.png

2020-10-23T19:43:33Z

Jpdiaz:

FIRMM

2020-10-23T17:05:57Z

Jpdiaz: create FIRMM software page and add Jared's instructional notes

==Framewise Integrated Real-time MRI Monitoring (FIRMM)==

'''Make sure Advanced User mode is enabled''' - You will know it is if the MARS_SSH shortcut is visible on the start menu

FIRMM Instructions:
#Press ctrl-esc on console --> STOP FIRMM Session
#Register your participant
#Press ctrl-esc on console --> START FIRMM Session
#Close out of terminal and X11 on iMac
#Double click "FIRMM.command" icon on desktop, this should open up terminal
#Type FIRMM into command line and press enter
#Terminal should start spitting out lines, X11 should open up and you should see a message on the terminal window that says "waiting for dicoms..."
#Click on the Start button on the X11 FIRMM application window, start your functional scan
#Volumes should start appearing after ~45sec delay

EEG

2020-10-22T00:28:23Z

Jpdiaz: /* Programs for EEG data processing */ add external links

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.
*[[General Pre-Processing Steps]]

===Programs for EEG data processing===
Standalone Applications
*[[Netstation]]
*[[BrainVision Analyzer]]
MATLAB Toolboxes
*[https://sccn.ucsd.edu/eeglab/index.php EEGLAB]
*[https://www.fieldtriptoolbox.org/ FieldTrip]
Python Packages
*[https://mne.tools/stable/index.html MNE]

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

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

*[[Under Construction]]

== Support ==
*[[EGI]]

== History ==

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