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    <image rdf:about="https://lncd.pitt.edu/wiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg">
        <title>LNCD</title>
        <link>https://lncd.pitt.edu/wiki/</link>
        <url>https://lncd.pitt.edu/wiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg</url>
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    <item rdf:about="https://lncd.pitt.edu/wiki/doku.php?id=grants:spa:anatomical&amp;rev=1787610795&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2026-08-24T22:33:15+00:00</dc:date>
        <dc:creator>vsydnor (vsydnor@undisclosed.example.com)</dc:creator>
        <title>UNI and R1 Preprocessing Pipelines</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=grants:spa:anatomical&amp;rev=1787610795&amp;do=diff</link>
        <description>UNI and R1 Preprocessing Pipelines

UNI PROCESSING PIPELINE

 

1. Run Hera/Projects/SPA/scripts/mri/preproc/00_bids-t1-only.bash to link Hera/Raw/BIDS/SPA/sub-$/ses-$/anat/*UNIT1* to Hera/Projects/SPA/scripts/mri/fs/bids-t1only

2. Run Hera/Projects/SPA/scripts/mri/preproc/01_denoise_unicort.bash</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-08-24T20:41:14+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Electroencephalogram (EEG)</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:eeg&amp;rev=1787604074&amp;do=diff</link>
        <description>Electroencephalogram (EEG)

EEG acquisition is part of SPA EEG, Habit EEG Protocol, 7T EEG.  Run in the lab space EEG at Loeffler with different caps.

All studies included the Anti @ EEG experiment.

Analysis includes Fitting Oscillations and 1/f (FOOOF), Spectral Event Pipeline, Signal to Noise Ratio (SNR)

Electrodes recorded into channels.
             Desc                      Mastoids</description>
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    <item rdf:about="https://lncd.pitt.edu/wiki/doku.php?id=tools:switchtask&amp;rev=1787233029&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2026-08-20T13:37:09+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Switch Task (MMY4, SPA) - [Practice Block] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:switchtask&amp;rev=1787233029&amp;do=diff</link>
        <description>Switch Task (MMY4, SPA)

Also known as  nBMSI  n-Back Multi-Source Interference. Original used MMY4 but with 3rd n-back trial type.

Code shared publicly at &lt;https://github.com/labneurocogdevel/MMY4&gt; written in matlab with Psychtoolbox and adapted for EEG with psycyhopy/python

Bart&#039;s 2016 WPIC poster on the task: [Brain state expression and cognitive flexibility in adolescence and young-adulthood]

MR

See</description>
    </item>
    <item rdf:about="https://lncd.pitt.edu/wiki/doku.php?id=tools:loefeeg:log&amp;rev=1787152049&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2026-08-19T15:07:29+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Loeffler EEG Log</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:loefeeg:log&amp;rev=1787152049&amp;do=diff</link>
        <description>Loeffler EEG Log

Log for EEG at Loeffler. Also see the dynamically generated log over full wiki Wiki Log

	*  2026-08-19 Record PC Error 5000 Optical fiber is disconnected forced visit reschedule 
		*  Optical cable box started in front USB port. Moved around without luck. After total tear down, font port worked again (w/o any electrodes, fiber cable only). Retested back port, did not work.</description>
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        <dc:date>2026-08-19T13:46:25+00:00</dc:date>
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        <title>20260819-094625.png - created</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?image=tools%3Aloefeeg%3Apasted%3A20260819-094625.png&amp;ns=tools%3Aloefeeg%3Apasted&amp;rev=1787147185&amp;tab_details=history&amp;media_do=diff&amp;do=media</link>
        <description>&lt;img src=&quot;https://lncd.pitt.edu/wiki/lib/exe/fetch.php?w=500&amp;amp;h=500&amp;amp;tok=a431c7&amp;amp;media=tools:loefeeg:pasted:20260819-094625.png&quot; alt=&quot;20260819-094625.png&quot; loading=&quot;lazy&quot; width=&quot;500&quot; height=&quot;500&quot; /&gt;</description>
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        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>EEG at Loeffler - [EEG at Loeffler] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:loefeeg&amp;rev=1787146848&amp;do=diff</link>
        <description>EEG at Loeffler

The current first-floor Loeffler building EEG collection first started in March-May 2022. And is used for Habit EEG Protocol (and maybe eventually SPA EEG). 7T EEG had some but not all data collected here. Both Habit and 7T data are stored in /Volumes/Hera/Raw/EEG/</description>
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        <dc:date>2026-08-07T20:38:28+00:00</dc:date>
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        <title>Habit Dollar Reward fMRI processing</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=grants:habit:mr:dollarreward&amp;rev=1786135108&amp;do=diff</link>
        <description>Habit Dollar Reward fMRI processing

Habit Study (R37) preprocesing of Habit MR&#039;s Dollar Reward

	*  preprocessing with fmriprep
	*  additional cleaning (smoothing, nuisance compute mhproc fMRI Preprocessing)
	*  first level GLM


cd /Volumes/Hera/Projects/Habit/mr
ls fmriprep/25.0.0*/sub-*/ses-*/func/sub-*_ses-*_task-dollarreward_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz</description>
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        <description>&lt;img src=&quot;https://lncd.pitt.edu/wiki/lib/exe/fetch.php?w=500&amp;amp;h=500&amp;amp;tok=7b2bda&amp;amp;media=grants:habit:mr:pasted:20260807-141837.png&quot; alt=&quot;20260807-141837.png&quot; loading=&quot;lazy&quot; width=&quot;500&quot; height=&quot;500&quot; /&gt;</description>
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        <title>20260807-141537.png - created</title>
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        <description>&lt;img src=&quot;https://lncd.pitt.edu/wiki/lib/exe/fetch.php?w=500&amp;amp;h=500&amp;amp;tok=3ca765&amp;amp;media=grants:habit:mr:pasted:20260807-141537.png&quot; alt=&quot;20260807-141537.png&quot; loading=&quot;lazy&quot; width=&quot;500&quot; height=&quot;500&quot; /&gt;</description>
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        <dc:date>2026-08-06T19:40:57+00:00</dc:date>
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        <title>Anti @ EEG - [Degree Visual Angle/Distance Measurements] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:antisaccade:eeg&amp;rev=1786045257&amp;do=diff</link>
        <description>Anti @ EEG

Anti@EEG is a version of Antisaccade Tasks originally developed for Brain Mechanisms R01 (7T).

The source is vgs_ant.py (Psychopy) part of Memory Guided Saccade (MGS) Task, same interface can also run Visually Guided Saccade Task.

Used in 7T EEG,  Habit EEG Protocol,  SPA EEG.

Dollar Reward&#039;s psychopy implementation can also be run with parallel port (LPT) Status channel triggers enabled for EEG recording.</description>
    </item>
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        <title>20260806-153510.png - created</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?image=tools%3Aantisaccade%3Apasted%3A20260806-153510.png&amp;ns=tools%3Aantisaccade%3Apasted&amp;rev=1786044910&amp;tab_details=history&amp;media_do=diff&amp;do=media</link>
        <description>&lt;img src=&quot;https://lncd.pitt.edu/wiki/lib/exe/fetch.php?w=500&amp;amp;h=500&amp;amp;tok=53ff98&amp;amp;media=tools:antisaccade:pasted:20260806-153510.png&quot; alt=&quot;20260806-153510.png&quot; loading=&quot;lazy&quot; width=&quot;500&quot; height=&quot;500&quot; /&gt;</description>
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    <item rdf:about="https://lncd.pitt.edu/wiki/doku.php?id=tools:eyetracking&amp;rev=1786041264&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2026-08-06T18:34:24+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Eye Tracking - [Configurations] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:eyetracking&amp;rev=1786041264&amp;do=diff</link>
        <description>Eye Tracking

See Antisaccade Tasks for general anti task description and notes. Specific tasks linked below

Tasks
 Task/Version       Where    Grants  Anti Antisaccade Task (Eprme) lab/ASL Eyetracker Cog Grant,  PET Study  Anti Antisaccade Task (Psychopy) lab/asl        Brain Mechanisms R01 (7T), Habit Study (R37), Synaptic Pruning Adolescence (SPA)  AntiState Mix   lab/ASL, MR/ASL    Cog Grant, PET Study, Brain Mechanisms R01 (7T), Habit Study (R37)  Dollar Reward (EPrime) MR/ASL, MR/Avotech …</description>
    </item>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-08-06T18:27:52+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Anti Antisaccade Task - [Visual Angle] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:antisaccade:anti&amp;rev=1786040872&amp;do=diff</link>
        <description>Anti Antisaccade Task

“Anti” is a Eye Tracking Antisaccade Tasks (not to be confused with “AntiState”  AntiState Mix) written in EPrime for ASL Eyetracker.

The task was used in Brain Mechanisms R01 (7T), behavioral visit of PET Study and Cog Grant (?)

Trials are like

	*  antifix -- red cross, variable {0.5,2,4,6} sec
	*  gap  -- blank, .2sec</description>
    </item>
    <item rdf:about="https://lncd.pitt.edu/wiki/doku.php?id=tools:infrastructure_cite&amp;rev=1785955743&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2026-08-05T18:49:03+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Infrastructure Citations</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:infrastructure_cite&amp;rev=1785955743&amp;do=diff</link>
        <description>Infrastructure Citations

For grant writing, see Grant Blurbs

MRRC

rrid:scr_025215

	&quot; 2. Please cite the MRRC in your publications. Research Resource Identifiers (RRIDs) are persistent and unique identifiers for research resources such as core facilities, organisms, tools, etc. More information can be found on this website:</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-08-05T18:43:06+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>CRC</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:crc&amp;rev=1785955386&amp;do=diff</link>
        <description>CRC

The Center For Research Computing is a pitt HPC (High performance computing) “super computer” resource behind the pitt firewall (see Global Connect for Remote Access).

The CRC is a smaller resource than the Pittsburgh Super Computer but with easier (no-grant-needed) access.

CRC has NIST-level computation (for e.g. ABCD) via secure enclave (</description>
    </item>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-07-31T18:07:38+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Habit MR - [Acquisitions/Scan sheet] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=grants:habit:mr&amp;rev=1785521258&amp;do=diff</link>
        <description>Habit MR

	*  Scan protocols are in 
	*  (out of date: )
	*  Using 32-channel head coil (vs 64). 
	*  Originally scanned only on Primsa 2. TODO: DATE, also scanning on Primsa 1. See REDCap field TODO: XXX. 
	*  The project started with Arrington/Avotec eye tracking. Most of year 2 and onward is using</description>
    </item>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-07-31T18:02:00+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Dollar Reward - [Dollar Reward] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:antisaccade:dollarreward&amp;rev=1785520920&amp;do=diff</link>
        <description>Dollar Reward

DollarReward/RingReward is rewarded and neutral Antisaccade Tasks task.

	*  was an EPrime task for Cog Grant (MR, behave) and later a Psychopy task for Habit Study (R37) (MR, EEG) and NCANDA (MR)
	*  Originally for ASL Eyetracker but adapted in psychopy for avotech and then Prisma SSR EyeLink
	*  Task source code is online and on bea_res</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-07-24T17:29:07+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Python in R</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:r:python&amp;rev=1784914147&amp;do=diff</link>
        <description>Python in R

reticulate is an R package that brings Python into R.


library(reticulate)

# use project specific python packages stored in folder created with
#    python -m venv .venv
use_virtualenv(&quot;.venv&quot;) # analogous to &#039;source .venv/bin/activate&#039;


The RStudio environment explorer (top right) shows python variables and</description>
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        <dc:date>2026-07-24T16:43:46+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>GNU R - [GNU R] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:r&amp;rev=1784911426&amp;do=diff</link>
        <description>GNU R

The GNU R programming language is often paired with posit&#039;s RStudio Desktop IDE and a suit of libraries (language packages) known as tidyverse (includes dplyr and ggplot2). R and RStudio (including Rmarkdown code cells) can use python interleaved with R code. See Python in R.

You can also find a web interface to Rstudio on rhea (also</description>
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        <dc:date>2026-07-20T14:31:24+00:00</dc:date>
        <dc:creator>vid79 (vid79@undisclosed.example.com)</dc:creator>
        <title>wpc-8620_20240320_wip.pdf - created</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?image=grants%3Ahabit%3Awpc-8620_20240320_wip.pdf&amp;ns=grants%3Ahabit&amp;rev=1784557884&amp;tab_details=history&amp;media_do=diff&amp;do=media</link>
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        <dc:date>2026-07-14T17:13:21+00:00</dc:date>
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        <title>Antisaccade Tasks - [EOG Data] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:antisaccade&amp;rev=1784049201&amp;do=diff</link>
        <description>Antisaccade Tasks

The LNCD has a collection of tasks varying how a participant should look away from or to a dot.

Scoring by Automatic Eye Scoring, see github readme citation section lab papers methods quotes. See Eye Tracking for camera hardware.


Fig 1. Anti-saccade task, taken from Luna et al, NeuroImage, 2001</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-07-14T17:01:10+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Automatic Eye Scoring - [7T] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:autoeyescore&amp;rev=1784048470&amp;do=diff</link>
        <description>Automatic Eye Scoring

R code to identify and score saccades along the horizontal meridian. 

Available in /Volumes/Hera/Projects/autoeyescore and on &lt;https://github.com/LabNeuroCogDevel/autoeyescore/&gt;

See github readme citation section for how this code is cited in manuscripts from the lab.

trialwise scoring includes

	*  trial number</description>
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