https://www.lncd.pitt.edu/wiki/ 2026-04-05T16:51:20+00:00 https://www.lncd.pitt.edu/wiki/ https://www.lncd.pitt.edu/wiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2025-02-19T21:33:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:adi&rev=1740000821&do=diff Area Deprivation Index (ADI) * ADI is obtained cross referencing Participant Address information with <https://www.neighborhoodatlas.medicine.wisc.edu/> * There are two ADIs- ranking neighborhoods within a state and within the nation. I (Maria) have typically used the national ranking one (scale of 1-100) because some of our participants are from out of PA. This is 'ADI_NATRANK' in text/html 2026-03-11T13:55:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:adm&rev=1773237313&do=diff ADM ASEBA ADM (Achenbach system of empirically based assessment: Assessment Data Manager) is a discontinued windows software package (circa 2015) used to manually input and score/provide ASR/YSR and cbcl results. Install From CD-ROM or iso on BEA_RES (L Drive) Applications/ASEBA-ADM_age18-59.iso text/html 2026-03-25T20:00:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:afni_gui&rev=1774468817&do=diff AFNI GUI AFNI's Graphical User Interface has a deep feature set. Slider You can slide between overlay and underlay. Enable this mode by pushing 3 or 4 with an image window focused. Graph View For underlays with a time dimension (multiple values), the text/html 2026-03-25T19:27:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:afni&rev=1774466876&do=diff AFNI Also see the AFNI GUI subpage for tips on the graphical interface. DataTable 3dMVM and 3dLME can take an input table like 3dMVM ... -dataTable @myfile.tsv. Both are very particular about the format of the input file. * Subj must be the name of the first column (and thus the first word of the file) text/html 2025-09-26T17:29:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:antisaccade&rev=1758907746&do=diff 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 text/html 2025-05-16T21:04:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:ants&rev=1747429466&do=diff ANTs Advanced Normalization Tools is a suite of tools for “spatial normalization” or warping or registration. Like fsl's flirt/fnirt or AFNI's 3dQwarp. (NB. resample like 3dresample is not warping). Among many other pipelines, ANTs is used by fmriprep to align per visit T1w images to the text/html 2025-07-03T17:27:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:asrysr&rev=1751563653&do=diff ASR/YSR Adult Self Report and Youth Self Report. CBCL is parent reported version for younger participants. Scored using ADM. Used as screening for MultiModal , PET Study, Brain Mechanisms R01 (7T), Habit Study (R37), and Synaptic Pruning Adolescence (SPA). Collected on paper, Qualtrics (see packets) and then REDCap. Local Data 7T Subscale summaries are in 7T Data: merge_7t.csv with the text/html 2025-01-13T15:39:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:asws&rev=1736782751&do=diff Adolescent Sleep Wake Scale For 7T BrainMech Qualtrics Survey translated from . Used with REDCap during SPA Behavioral Visit. Also see Sleep Timing Questionnaire. Scoring /Volumes/Hera/Projects/7TBrainMech/scripts/behave/ASWS.R (git backup) makes /Volumes/Hera/Projects/7TBrainMech/scripts/behave/txt/asws.csv based on <https://www.colorado.edu/lab/sleepdev/sites/default/files/attached-files/appendix_asws.docx> also see <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201644/> text/html 2024-11-11T14:16:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:auditorysteadystate&rev=1731334605&do=diff Auditory Steady State Response During auditory steady state, participants are presented with a blank screen and hear a train of clicks in stereo with headphones. The stimulus is presented in blocks of 150 trials. Trials consists of 500ms of click train and 605ms of silence. Blocks are repeats of either 10 20Hz click, 15 30 Hz click, or 20 40 Hz click trains. Block order is randomly assigned (e.g., 30-40-20). The task is written in and executed by NBS Presentation software. text/html 2025-01-08T17:10:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:autoeyescore&rev=1736356205&do=diff Automatic Eye Scoring R code to identify and score saccades along the horizontal meridian. Available in /Volumes/Hera/Projects/autoeyescore and on <https://github.com/LabNeuroCogDevel/autoeyescore/> See github readme citation section for how this code is cited in manuscripts from the lab. trialwise scoring includes * trial number text/html 2026-03-11T15:44:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:bea_res&rev=1773243850&do=diff BEA_RES (L Drive) The lab has PII-allowed UPMC-firewalled file storage through the Office of Academic Computing (OAC). Colloquially, this is the “L drive” as it is mounted to L:\ on Windows PCs. For getting account access, see OAC groups (LDAP). The directly of the slashes in the address for the file share depends on the operating system. For windows text/html 2023-10-21T14:28:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:bfg&rev=1697898531&do=diff BFG: git Repo Cleaner As mentioned in github docs, BFG is the prefered way to scrub secrets, credentials, PHI, and other sensitive information accidentally included in a git repo. (avoid git -A and you're unlikely to end up in this situation) On rhea us the command: text/html 2024-03-15T16:23:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:bids_apps&rev=1710519839&do=diff New to BIDS? Check out resources on the Brain Imaging Data Structure <https://bids.neuroimaging.io/> A list of useful software containers that work on BIDS-formatted data (BIDS apps): Freesurfer: <https://github.com/bids-apps/freesurfer> fMRIPrep: <https://fmriprep.org/en/stable/> QSIPrep: <https://qsiprep.readthedocs.io/en/latest/index.html> SPM: <https://github.com/bids-apps/SPM> and <https://github.com/cpp-lln-lab/bidspm> MRTrix3: <https://github.com/bids-apps/MRtrix3_connectome> … text/html 2025-07-21T15:49:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:bids&rev=1753112951&do=diff BIDS The Brain Imaging Data Structure is a specification for how to organize and name imaging files. The homepage is <https://bids-specification.readthedocs.io/>. The entities table is a dense and complete description of the information contained in BIDS. Files are organized with names that have _ separated text/html 2025-07-03T17:25:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:bird&rev=1751563532&do=diff Behavioral Indicator of Resiliency to Distress (BIRD) 7T 7T Behavioral Protocol /Volumes/Hera/Projects/7TBrainMech/scripts/behave/BIRD_110122.RData text/html 2025-10-24T16:11:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:c3d&rev=1761322286&do=diff convert3d c3d is a tool from itksnap used by hippunfold, Preprocess Functional (Hallquist pipeline) (and in their own container by fmriprep and friends). As of 2025-10-24 on Rhea (linux server), c3d is vs 1.4.4. Updated from 2017 install b/c hippunfold requires -retain-labels option. readlink /opt/ni_tools/c3d # itksnap/c3d-1.4.4-Linux-gcc64/bin/ text/html 2026-03-11T14:38:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:cantab&rev=1773239934&do=diff Cambridge Neuropsychological Test Automated Battery (CANTAB) CANTAB provided a suit of “games” (DMS, MOT, SOC, SSP) that participants interacted with using a clear touch screen placed on top of a CRT monitor. When the desktop application was discontinued, we switched to text/html 2024-07-24T13:39:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:choosing_k_for_age_smooths_in_generalized_additive_models&rev=1721828341&do=diff A Practical Guide to Choosing the Value of k for Age Smooths in Generalized Additive (Mixed) Models Background GAM smooth functions and splines When using GAMs (or GAMMs) to model neurodevelopmental trajectories, we model age as a smooth term: model <- gam(brain ~ s(age), method = "REML") text/html 2025-06-03T20:45:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:cifti_surfaces&rev=1748983539&do=diff Surface-based Analysis (cifti) Surface files track vertices instead of volumetric voxels. Files are created by tools like xcpd. Types citfi files have double extentions like *.dscalar.nii. See <https://balsa.wustl.edu/about/fileTypes> for more. From there, highlights are: dscalar one or more dense maps of scalar values (e.g., myelin maps, curvature maps) text/html 2025-06-18T13:03:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:clocktask&rev=1750251802&do=diff Clock Task MATLAB/pyschtoolbox task code is available on github:CogEmoFaceReward. It was developed for MultiModal/MultiModal Year 4 (2015). Additional usage and development continued by DNPL and dependlab (Dombrowski, Hallquist), including a port to Millisecond Inquisit and 2025 publication. For MEG timing, a corner box flashes black/white to encode event display onsets with a text/html 2025-08-25T18:46:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:codereview&rev=1756147593&do=diff Code Review A part of the LNCD Data Club. * topic/presenter schedule on office sheet * See the github repo at <https://github.com/LabNeuroCogDevel/lncd_dataclub/> and included readme for a detailed guide. * original topic list, interest forum See Git and especially adding ssh keys as well as GitHub CLI Links * <https://trishagee.com/presentations/code_review_best_practice/> * CodeReview pdf from Knight Lab (BioInformatics@UCSD) * also links text/html 2024-04-24T15:38:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:crc&rev=1713973085&do=diff 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 access. text/html 2025-10-13T13:39:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:cspine&rev=1760362791&do=diff CSpine * On github <https://github.com/LabNeuroCogDevel/cspine-pointer> * On rhea /Volumes/Hera/Projects/cspine-pointer * Default outputs stored in /Volumes/Hera/Projects/cspine-pointer/output with file names defaulting to mirroring input like sub-11275_ses-20160519_acq-1ADNIG2_run-2_T1w_cspine-lncd_create-2024-10-31T154517.tsv text/html 2025-04-24T14:30:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:datalad&rev=1745505011&do=diff Datalad Datalad is a git-annex wrapper useful retrieving external datasets as well as for Code Documentation. Repos Useful repos using datalad include * TemplateFlow (templateflow datalad docs) * Reproducible Brain Chart (includes PNC among others) text/html 2025-11-17T19:12:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:daw&rev=1763406770&do=diff Daw Sequential Learning “Two-Step” Task Collected during Habit Behavioral Protocol and 7T Behavioral Protocol. Code from From Creatures of Habit to Goal-Directed Learners: Tracking the Developmental Emergence of Model-Based Reinforcement Learning, Decker 2016 Task written in MATLAB/Psychtoolbox. Administering L:\Administrative\RA training documents\Habit Behavioral Instructions Running the DAW Task - Open MATLAB * Navigate to L:\Tasks\Daw_TwoStep_SequentialLearning text/html 2023-09-19T14:09:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:db&rev=1695132595&do=diff LNCD Database <https://github.com/LabNeuroCogDevel/db_from_sheets/> The perpetually in-development database. PostgreSQL created from qualtrics and participation flow spreadsheets. LNCD Tools provides convince functions lncddb $query, selld8 l, and ld8info $ld8 $ld8 text/html 2026-03-11T18:58:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:demographics&rev=1773255515&do=diff Demographics A survey with questions on education, income (social economic status), ethnicity, and race. For 7T, see BEA_RES (L Drive)'s IRB docs <\\acct.upmchs.net\bea_res\Administrative\IRB\STUDY19030154_7T\2021\7T x3 Mod\Last approved version\BaselineDemographicForm_revised 2018_Version_0.01.doc> text/html 2024-11-09T18:32:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:ders&rev=1731177142&do=diff Difficulties in Emotion Regulation Scale Collected in SPA Behavioral Visit (REDCap) text/html 2025-10-28T19:49:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:docker&rev=1761680982&do=diff Docker Docker containers are one way of establishing a fixed software environment. This is ideal for sharing the exact version and setup used for running your project. Using see fmriprep's docker documenation Hints * Use bind mounts to map an actual path to a virtual one within the container like text/html 2025-04-26T02:06:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:duq&rev=1745633165&do=diff Drug Use Questionnaire (DUQ) In Habit Behavioral Protocol and SPA Behavioral Visit in REDCap for both and some of habit timepoint one in Qualtrics. For habit, see /Volumes/Hera/Projects/Habit/behave/duq.csv Alternative DUQ does not ask about nicotine. ASR/YSR does. habit_redcap_dict$data|> mutate(Q=gsub('<[^>]*>','',field_label)) |> # remove html select(field_name, Q) |> filter(grepl("nicotine|vape|smoke",Q, ignore.case=T))|> print(n=Inf) text/html 2024-12-03T19:34:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:eeg_7t_preprocessingpipeline&rev=1733254440&do=diff EEG Preprocessing Pipeline for 7T/BrainMechR01 Concurrent EOG and high-impedance EEG was recorded with a Biosemi ActiveTwo with Actiview software (Minimitter, Bend, OR) 64-channel EEG system, in accordance with the international 10–20 system (Neymotin et al., 2020), located in an electromagnetically shielded room while participants performed the MGS task (described above). The task stimuli were presented on a computer 80 cm from the subject, and head position was maintained using a chin rest. I… text/html 2025-10-24T20:40:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:eeg_remark&rev=1761338404&do=diff EEG Remarking Status Channel “Remarking” is part of the preprocessing pipeline. For more see EEG Preprocessing Pipeline for 7T/BrainMechR01 Why The BioSemi device used in EEG at Loeffler records in 24-bits on the Status Channel (16 available for task). Matlab and python read in 32-bits. Task “trigger”/“TTL” values in the Status channel are read in offset from what is sent/intended-to-be-recorded. More info about the BDF format on text/html 2024-03-15T15:54:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:eegcoordinates&rev=1710518054&do=diff EEG Coordinates * Open MATLAB, run brainstorm * Use default anatomy ICBM 152 * File > new subject > use default anatomy * Import EEG * Can select all data or just one trigger type * Right click on subject > Review raw file > Imports raw data text/html 2023-11-09T17:53:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:emacs&rev=1699552415&do=diff Emacs Emacs is an actively developed open source text editor for code and prose old enough to have heirloom configuration files. It has it's own wiki and stack exchange Emacs advocates point to the lindy effect and GNU community roots to argue Emacs is a safe investment. While, detractors point to the need for investing time to learn as a reason to avoid Emacs. text/html 2024-09-06T15:17:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:entropy&rev=1725635843&do=diff Entropy text/html 2024-11-11T14:33:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:eprime&rev=1731335618&do=diff EPrime E-Prime is a commercial experiment builder. The original Antisaccade Tasks were made and run with E-Prime. As of EPrime3, UPitt no longer has access to a department-provided version. New tasks are developed with the open source Psychopy. Backlink Wiki pages linking here should include tasks using EPrime. text/html 2025-09-26T17:36:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:eyetracking&rev=1758908203&do=diff 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 … text/html 2026-03-19T18:36:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:fmri_preproc&rev=1773945369&do=diff fMRI Preprocessing This page is a generic overview. For specific software see * fmriprep + xcpd -- BIDS App standard functional MRI preprocessing * Preprocess Functional (Hallquist pipeline) -- in-house legacy pipeline from Hallquist. Has useful features and exists for older studies (Cog Grant, PET Study, Brain Mechanisms R01 (7T)) Considerations: text/html 2026-03-19T18:44:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:fmriprep&rev=1773945857&do=diff fmriprep Find full documentation on <https://fmriprep.org/en/stable/> Also see fMRI Preprocessing, Preprocess Functional (Hallquist pipeline) Follow up fmriprep outputs (*_desc-preproc_bold.nii.gz) with xcpd. Example usage: * Hera/Projects/Habit/mr/fmriprep_habitstudy.bash Considerations * fmriprep can reuse freesurfer when run before (otherwise will run minimal version internally). text/html 2023-11-09T19:51:49+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:fooof&rev=1699559509&do=diff Fitting Oscillations and 1/f (FOOOF) Please refer to the FOOOF Github Repository for detailed methods of the FOOOF toolbox and to our own LNCD FOOOF Code The Fitting Oscillations and 1/f (FOOOF) protocol derives the 1/f spectral slope (referred to as the aperiodic exponent) and an offset. The steepness of the slope (i.e., the exponent) has been previously linked to shifts in the text/html 2025-04-01T21:07:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:freesurfer&rev=1743541632&do=diff FreeSurfer is a software suite for processing, analyzing, and visualizing human brain structural MRI images. It generates processed volumetric and surface data in subject native space. The main workhorse of Freesurfer is recon-all, which is discussed in Andy's Brain Book. There are modifications on recon-all for text/html 2024-09-06T16:33:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:frogger&rev=1725640401&do=diff Frogger Task text/html 2026-03-04T20:09:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:gam&rev=1772654966&do=diff GAM Generalized Additive Models (and Generalized Additive *Mixed* Models) for non-linear relationships. See * QCBS R Workshop Series * A recipe for accurate estimation of lifespan brain trajectories, distinguishing longitudinal and cohort effects for “various ways of formulating GAMMs for estimation of lifespan trajectories of 12 brain regions, using a large longitudinal dataset text/html 2024-08-18T00:55:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:gh&rev=1723942544&do=diff GitHub CLI gh can bin installed with instructions from <https://github.com/cli/cli#installation> It's useful for Code Review. Also see <https://github.com/magit/forge> Equivalent tools for other forges exist: gitlab.com has lab, gitea has tea, hut for source hut. text/html 2025-10-16T15:07:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:git&rev=1760627279&do=diff Git git is a “distributed version control system” (dVCS) or “source control management” (SCM) tool used to track changes, primarily for source code in text files. git has command line and graphical interfaces. Alternative SCM tools include fossil, text/html 2025-12-12T20:33:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:github&rev=1765571617&do=diff Github setup Github (source forge) is not git (local-first distributed source control management software)! See Git for using git. Github setup includes * or an existing remote github repository url * use ssh url like git@github.com:group/repo text/html 2024-06-05T10:53:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:globalconnect&rev=1717584783&do=diff Global Connect Virtual Private Network (VPN) to connect to PittNet. See pitt's instructions. openconnect is an open source alternative that works with the global protect infrastructure, and can be partially automated (<https://github.com/WillForan/dotconf/blob/master/bin/openconnect-pitt> still needs Duo MFA) For UPMC's network, see MyApps in text/html 2024-04-24T15:34:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:globus&rev=1713972854&do=diff Globus Connect <https://www.globus.org/globus-connect> is a `GridFTP` service that can “connect many different storage types to transfer and share data.” It's useful for getting data to and from CRC. rsync might be a better choice for Pittsburgh Super Computer, but globus is a good solution for transfer lots of data there too. text/html 2023-11-10T17:07:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:gordonatlas&rev=1699636055&do=diff Gordon Atlas The Gordon atlas is a cortical parcellation atlas comprised of 333 cortical areas (across left and right hemispheres). The Gordon atlas was derived in Gordon et al., 2016, Cerebral Cortex based on resting state functional connectivity boundaries. Different versions of the atlas are available that have the text/html 2024-11-11T19:20:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:gordonharoxatlas&rev=1731352820&do=diff Gordon + Harvard-Oxford Atlas An atlas that combines Gordon Atlas and haroxatlas rhea:/opt/ni_tools/atlas/GordonHarOx/Gordon_HarOx_1mm+tlrc.HEAD The first 333 are Gordon Atlas, the next 12 are from harox (numbered 333+1:12 -- not matching original harox value) roiorig values L,R in combined text/html 2025-12-05T19:23:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:habittask&rev=1764962624&do=diff Reward Learning and Habituation Task for Habit Study (R37) on github <https://github.com/LabNeuroCogDevel/choice-landscape> A static playable version without external recordings is hosted on github <https://labneurocogdevel.github.io/choice-landscape/> Shane ported the task to Psychtoolbox for Habit sEEG Protocol Documentation on coalesced and parsed parsed data on Habit Task Data Parsing. /Volumes/L/bea_res/Data/Tasks/Habit/MR/11734_20221111/sub-11734_task-mr_habit_ses-20221005_run-1_1668… text/html 2025-06-16T16:01:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:hairhormones&rev=1750089691&do=diff Hair Hormones * For Brain Mechanisms R01 (7T) results see 7T Data: merge_7t.csv's column Cortisol_hairconcentration_pgmg * raw data in /Volumes/Hera/Projects/7TBrainMech/scripts/txt/ or bea_res/Data/Hair/7TBrainMech/ * 7T_haircortisol.csv is Y1_hair_data_06082020.xlsx, BeaLunaBatch3_Master file_02.28.2023.xls text/html 2025-09-16T00:13:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:hc&rev=1757981627&do=diff MRSI in HC @ 7T (scripts) * Hippocampus Coordinates * script directory: /Volumes/Hera/Projects/7TBrainMech/scripts/mri/Hc * matlab gui program (from MRRC/Victor, Hoby): /home/ni_tools/matlab_toolboxes/MRRC/SVR1HFinal/SVR1H2015.fig * LC Model Review from 2024-12-09: * 230 visits in text/html 2024-06-04T14:51:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:highresolutionlogos&rev=1717512661&do=diff For Pitt logo: <https://www.brand.pitt.edu/downloads> For LNCD logo: /Volumes/L/bea_res/Administrative/Coversheets_Letterheads_Logos/Logo options/ Note: In directory above, Banner_logo_new.pdf contains University seal + LNCD logo. text/html 2026-02-17T18:17:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:hippunfold&rev=1771352262&do=diff Script that runs through the directory to find and save dice scores to a csv file lives here /Volumes/Hera/Projects/hippunfold/output_1mm/quality_check/01_hippunfold_qc.sh #output directory and file output_dir="/Volumes/Hera/Projects/hippunfold/output_1mm/quality_check" output_file="${output_dir}/hippunfold_qc.csv" #set up header echo "Subject,Session,DiceScore_left,DiceScore_right" > ${output_file} # goes through and finds the sub and ses for qc_folder in /Volumes/Hera/Projects/hippunfold… text/html 2023-11-21T14:48:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:htop&rev=1700578090&do=diff htop htop is an enhanced and more interactive top. It is a terminal user iterface that shows processes memory and cpu usage. You might use this to see how busy rhea is before launching a bunch of jobs/threads or otherwise allocating a large cpu pool. Also see `iotop`, text/html 2025-04-11T20:29:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:hurst_exponent&rev=1744403351&do=diff Hurst Exponent 2025 DW using xcpd on Brain Mechanisms R01 (7T) and Habit Study (R37) data. 2024 7T MP Using Preprocess Functional (Hallquist pipeline) preprocessing of Brain Mechanisms R01 (7T) data. Written by Maria Perica, 3/22/24, updated 6/24/24 to include dataset file paths The Hurst exponent is a measure of trends within time series over time, or the long-term memory/self-similarity of a time series. The value of the Hurst exponent can tell you how predictable future values of a time… text/html 2025-12-19T19:45:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:hvlt&rev=1766173530&do=diff Hopkins Verbal Learning Task (HVLT) From sciencedirect " A list of 12 items from three semantic categories is presented across three trials, followed by recognition testing. A modification of the original HVLT provides for an assessment of delayed recall prior to recognition in order to assess forgetting over time. text/html 2024-04-30T13:14:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:infrastructure_cite&rev=1714482878&do=diff Infrastructure Citations MRRC rrid:scr_025215 " 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: text/html 2025-07-21T16:58:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:inquisit&rev=1753117136&do=diff Millisecond Inquisit For lab specific licensing, see Millisecond Inquisit (account). replaces Cambridge Neuropsychological Test Automated Battery (CANTAB) and nih_toolbox in previous studies. Tasks Stop Signal 10 min Habit, SPA Four Choice Reaction Time 3 min Habit, SPA Tower of London 10 min Habit, SPA Category Switch 10 min text/html 2025-07-03T17:17:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:ius&rev=1751563030&do=diff Intolerance of uncertainty scale (IUS) Collected in PET Behavioral Protocol, see packets Aversion to uncertainty or unknown outcomes will be assessed using the intolerance of uncertainty short form scale, a 12-item questionnaire. text/html 2023-11-09T19:13:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:lcmodel&rev=1699557217&do=diff LC Model LCModel was utilized to quantify the spectral data (in the range of 1.8–4.0 ppm) (Provencher, 2001), which consist of default macromolecule components and 14 basis metabolite functions (N-acetylaspartate (NAA), N-acetylaspartylglutamate (NAAG), aspartate, lactate, creatine (Cre), γ-aminobutyric acid (GABA), glucose, glutamate (Glu), glutamine, glutathione, glycerophosphorylcholine (GPC), phosphorylcholine (PCh), myoinositol, and taurine). LCModel outputs contain Cramer-Rao Lower Bounds… text/html 2026-01-05T15:46:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:llm&rev=1767627978&do=diff Large Language Models As of 2025-12, Pitt has resources on AI Tools in at least two places * Knowledge Base/Communication and Collaboration/AI Tools * Service Catalog / Generative AI (GenAI) Tools And has access to 3 model providers * Copilot via github->MS->OpenAI (upload photo ID). Apply on github * Claude via anthropic * “Any sensitive or proprietary data that you upload to Claude is secure unless you share it with another user text/html 2024-04-18T14:17:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:lncd_mni_2018&rev=1713449877&do=diff lncd MNI 2018 (grid size mismatch) An fsl bug created 2mm and 2.3mm resampled MNI temples with an extra row of zero voxels in the image. (original 1mm was unmodified/unaffected). This off-by-one template was used for Cog Grant and PET Study. The correct MNI template is used for preprocessing text/html 2026-03-11T18:58:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:lncdbot&rev=1773255515&do=diff LNCD Bot The lncd chat bot emerged out of lockdown-era good morning route randomizer (“slack theme”). It now (2023-10-27) sends weekly * allscripts version control digests to #codereview * recent wiki changes to #wiki This is run from foranw@rhea's Cron text/html 2023-09-19T14:09:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:lncdtools&rev=1695132595&do=diff LNCD Tools see readme on <https://github.com/LabNeuroCogDevel/lncdtools> for details and install instructions. utilities and conveniences for: * BIDS * make * AFNI * Shell text/html 2024-11-16T19:30:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:loef_simulator&rev=1731785404&do=diff Loef Simulator (Mock Scanner) The scanner simulator in the loeffler building includes mock scanner sounds and motion tracking/training using MoTrak Scheduling Use the dedicated google calendar to block time. Use the ical link to import into outlook https://calendar.google.com/calendar/ical/de0e0mhr8q94dff5j1osjsrkd0%40group.calendar.google.com/public/basic.ics text/html 2025-10-28T21:01:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:loefeeg&rev=1761685315&do=diff 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/ text/html 2025-05-14T20:15:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:make&rev=1747253729&do=diff make make (specifically GNU make) only updates upstream dependencies of files that have changed based on modification time of the “source” and “destination” file. source and destination are defined by rules in the file named Makefile in the current working directory. Other build tools include google's text/html 2025-09-26T18:27:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:mgs&rev=1758911237&do=diff Memory Guided Saccade (MGS) Task Desc In Brain Mechanisms R01 (7T) from Ashley Code * <https://github.com/LabNeuroCogDevel/mgs_encode_memory.py> * /Volumes/L/bea_res/Tasks/Behavorial/mgs-beakid Projects * Cog Grant? * Habit Study (R37) - yellow dot cue, target help to vgs position after blank recall * Brain Mechanisms R01 (7T) - cue includes image for recall later, no helper text/html 2026-01-07T16:50:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:mobaxterm&rev=1767804619&do=diff MobaXterm MobaXterm is a terminal emulator that bundles an X11 server (using Cygwin). Useful for connecting to Rhea (onboarding) for among other things Creating Brain Images for Participants An alternative is to use the Remote Desktop Connection app launched from the start menu. Rhea Hostname rhea.wpic.upmc.edu text/html 2024-03-22T19:17:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:models_that_disaggregate_between_and_within_person_effects&rev=1711135043&do=diff Disaggregating Between and Within Person Effects created on 3/22/24 by Maria Perica While cross-sectional data is able to tell us about between-person effects, only longitudinal data can provide information about within-person effects. It is important to note that between-person effects do not necessarily generalize to within-person effects - classic example: at the between-person group level, people are more likely to have a heart attack if they exercise less, but at the within-person level, text/html 2025-03-03T15:15:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:motrak&rev=1741014936&do=diff MoTrak - Loeffler Simulator Motion Tracking Loef Simulator (Mock Scanner) uses Psychology Software Tools (makers of eprime) motrak setup. It's old and originally from the now defunct MRRC simulator. The software manual is here. Running Overview We schedule up to 15 minutes (SPA Behavioral Visit, Habit Behavioral Protocol) of simulation time for each visit. text/html 2025-05-16T17:33:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:mp2rage&rev=1747416780&do=diff MP2RAGE MP2RAGE is the anatomical MR acquisition used for BST3 7T Projects: 7T Anatomical Acquisitions and SPA MR. Processing has included running UNICORT before providing the images to freesurfer (MTR SNR, Hc Myelin), see Freesurfer for BrainMechR01 (7T). From the BIDS description " The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ( text/html 2025-07-21T15:56:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:mr_motion&rev=1753113413&do=diff MR Motion Also see * MoTrak - Loeffler Simulator Motion Tracking * QC: Quality Checking 4D Echo Planar Image Often measured with framewise displacement by measuring measure rotation and translation from one volume to the next. FD and raw rot and trans values are an output of frmiprep. Useful for all EPI, including dwi, task and text/html 2024-02-24T18:03:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:mrsicoordmover&rev=1708797802&do=diff MRSI ROI Coordinate placement tool Manually position ROIs for LC Model. Input slice likely positioned with MRSI Slice Positioning tool (QPASA). Code on github <https://github.com/LabNeuroCogDevel/MRSIcoord.py/>. Used for Brain Mechanisms R01 (7T) and Synaptic Pruning Adolescence (SPA). Also see PFC ROI Placement ROIs Maria's 13 ROIs. (TODO: enumerate. point to location on rhea) text/html 2025-09-15T16:42:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:mt&rev=1757954533&do=diff MT Magnetization Transfer ratio from a two sequence (MT/noMT) MRI during PET MR where MT/noMT pairs were repeated before and after task. /Volumes/Phillips/mMR_PETDA/scripts/MT 3dcalc -overwrite \ -prefix MTR1.nii.gz \ -m $MT \ -n $noMT \ -a $anat \ -expr '(1-m/n)*bool(a)' ... 3dcalc -prefix MTR_pdiff.nii.gz \ -o MTR1.nii.gz -t MTR2.nii.gz \ -expr '(t-o)/o' text/html 2025-04-22T17:10:52+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:neuromelanin&rev=1745341852&do=diff Neuromelanin Acquisition Analysis Code * <https://github.com/LabNeuroCogDevel/NM_toolbox> text/html 2023-09-19T14:09:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:nic&rev=1695132594&do=diff NIC * costs sheet * Proposal/Description document * tech lead job post * Flywheel: diagram, folder text/html 2026-03-10T14:46:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:nnunet&rev=1773153984&do=diff nnUNet From <https://github.com/MIC-DKFZ/nnUNet> initially (2026-03) for CSpine. " nnU-Net is a semantic segmentation method that automatically adapts to a given dataset." Use <https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/dataset_format.md> " [Input] Datasets consist of three components: raw images, corresponding segmentation maps and a dataset.json file specifying some metadata. text/html 2025-04-11T20:26:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:nonfactionaltoolbox&rev=1744403200&do=diff Nonfactional Matlab Toolbox (for hurst exponent) Matlab code to calculate the Hurst Exponent. The toolbox code is on github @ <https://github.com/wonsang/nonfractal> Example usage for Trakoshis et al eLife 2020 is also on github <https://github.com/elifesciences-publications/ei_hurst> Parameters lb (input to fminbnd(@(x)likelihood(...),lb,ub,...)) matters! All zeros ts with default text/html 2023-12-28T00:55:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:notes&rev=1703724922&do=diff Note Taking Tools In addition to Wiki (tool), personal note taking tools used in the LNCD include: * bea: composition notebook * shane: giant word doc (-2022), evernote (2022-) * will: zim-wiki (2011-), emacs-zimwiki-mode (2019-) TODO: other's note strategies. Other software There's a ton of interesting note taking software. Ideally, notes are accessible in perpetuity text/html 2024-03-26T16:44:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:pfc&rev=1711471463&do=diff PFC ROI Placement ROI placement on top of PFC scout preformed manually. PFC slice orientation at acquisition is positioned by MRSI Slice Positioning tool (QPASA). For files organization see 7T MRSI PFC Files. How to place coordinates You will have 2 windows open simultaneously: coordinate placing GUI text/html 2026-03-25T19:57:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:preprocessfunctional&rev=1774468656&do=diff Preprocess Functional (Hallquist pipeline) * <https://github.com/LabNeuroCogDevel/fmri_processing_scripts> * <https://zenodo.org/badge/latestdoi/5274327> Developed by Michael Hallquist Output 4D nifti prefix As the pipeline progresses it outputs files with distinct prefixes that describe each step in reverse order. e.g. final output might be brnwsdktm_func_4.nii.gz text/html 2025-08-04T18:38:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:preprocessmprage&rev=1754332730&do=diff preprocessMprage (Hallquist pipeline) preprocessMprage is a prerequisite for Preprocess Functional (Hallquist pipeline). Code is <https://github.com/LabNeuroCogDevel/fmri_processing_scripts/> and on rhea in /opt/ni_tools/fmri_processing_scripts. It is analogous to smriprep: skullstrips and MNI-aligns the anatomical/structural T1w image. Important files include: text/html 2024-11-11T14:26:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:presentation&rev=1731335179&do=diff NeuroBS Presentation <https://www.neurobs.com/> * Yearly licensed software for task presentation with precision timing. ($310/year; $40/30 days) * Popular for EEG. * Inhered from Peter Bauckman Auditory Steady State Response * Also used by Brain Coffmen/Dean Salisbury. * Alternatives: Psychopy (python) text/html 2025-08-18T14:44:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:project_reproducibility_guides_with_gh-pages&rev=1755528245&do=diff Creating a Reproducibility Guide using Github Pages Let's do reproducible science! We can create a Github Page that goes along with our project repo (our project code on github) that walks others through our project, code, analyses, and how to reproduce or implement all code associated with a given publication. text/html 2024-09-06T15:29:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:projectstemplate&rev=1725636544&do=diff Project Template Project Lead: Project Start Date: Current Project Status: Datasets: Github Repository: Publication DOI: Conference Presentations Code Documentation text/html 2024-12-09T19:15:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:psc&rev=1733771730&do=diff Pittsburgh Super Computer General information * To log in to the supercomputer ssh userid@bridges2.psc.edu. * For graphical apps (eg. AFNI), see SSH Display Forwarding (X11) * This is world accessible and total independent for either the pitt or UPMC network. no myapps, text/html 2024-11-11T14:36:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:psychopy&rev=1731335774&do=diff Psychopy Psychopy is a desktop application and python library for developing tasks (“games”), presenting stimuli. Though we have not taken advantage of the integration, psychopy links to the Amazon Turk alternative <https://pavlovia.org/>. It's a free and open source alternative to text/html 2024-11-11T14:30:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:psychtoolbox&rev=1731335405&do=diff Psychtoolbox psychtoolbox is a MATLAB toolbox (library) for creating tasks (“games”) and presenting stimuli. It occupies the same space as Psychopy EPrime, NeuroBS Presentation, and Millisecond Inquisit. Backlinks Wiki pages linking here should include tasks built with psychtoolbox: text/html 2025-05-13T17:59:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:puberty&rev=1747159196&do=diff Puberty Measures Also see specific measures tanner and peterson 7T For Brain Mechanisms R01 (7T), collected during 7T BrainMech Qualtrics Survey and included in 7T Data: merge_7t.csv /Volumes/Hera/Projects/7TBrainMech/scripts/behave/Makefile has the recipe txt/puberty.csv: svys.RData ./puberty_from_rdata.R where puberty_from_rdata.R text/html 2023-09-19T14:09:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:python&rev=1695132574&do=diff Python text/html 2025-09-15T16:33:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:qc&rev=1757954007&do=diff QC: Quality Checking Various data have been manually/visually inspected. * PFC ROI Placement - tracked using google sheets, elsewhere individual MRSI spectrums inspected. * 7T MR Quality Check - MP2Rage alignment (skull stripping) * MT/noMT multi sequence quality and alignment checks (PET Study) * Neuromelanin - * text/html 2024-02-24T18:02:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:qpasaslicewarp&rev=1708797723&do=diff MRSI Slice Positioning tool (QPASA) QPASA is a python Tk GUI to position a consistent acquisition for MRSI Acquisition * Code hosted on github, citation from zenodo * After acquisition, we use LC Model to metabolite concentration for specific ROIs. ROIs are manually positioned using text/html 2024-03-15T15:36:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:qsm&rev=1710516985&do=diff QSM TODO: WRITE ME text/html 2024-11-09T15:39:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:qualtrics&rev=1731166756&do=diff Qualtrics Qualtrics is a web platform for distributing and administering digital surveys to participants. It's used for 7T BrainMech Qualtrics Survey and habit, replaced with REDCap for SPA Behavioral Visit and Y2 onward for Habit Behavioral Protocol. Creating Accounts Free accounts (e.g. @upmc.edu) collaborate with the surveys owned by the main pitt account. text/html 2025-07-21T16:15:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:quic&rev=1753114540&do=diff Questionnaire of Unpredictability in Childhood (QUIC) Collected in SPA Behavioral Visit. Expected to take 10mins to complete. text/html 2025-11-21T21:25:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:r&rev=1763760335&do=diff GNU R The GNU R programming language is often paired with posit's RStudio Desktop IDE and a suit of libraries (language packages) known as tidyverse (includes dplyr and ggplot2). You can also find a web interface to Rstudio on rhea (also Remote Access). Tutorials contains additional resources. See * R Issues for log of debugged problems. * R versions for using specific older versions text/html 2024-03-15T16:12:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:r2prime&rev=1710519176&do=diff R2' Measure of Tissue Iron concentration. * Valur Olafsson developed gradient descent algo w/TSE and GRE sequences on mMR * published Dopamine-related striatal neurophysiology is associated with specialization of frontostriatal reward circuitry through adolescence * ported to prisma <https://github.com/LabNeuroCogDevel/r2prime-prisma> * part of Forbes' Adept LEAP, shared with Manuel Kuhn (Diego Pizzagalli, harvard) * see Pallidum => highest intensity iron signal text/html 2025-04-30T20:15:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:raid&rev=1746044119&do=diff RAID Redundant Array of Independent Disks is a technique to combine hard drives to a single large storage pool and protect against single drive failures. * Zeus RAID6 - megaraid hosted on rhea * Hera - NAS and RAID6 host * Phillips RAID6 text/html 2025-02-10T20:19:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:rest&rev=1739218763&do=diff Resting State Task MR For Habit Study (R37) and Synaptic Pruning Adolescence (SPA): Eyes open, projector off (no fixation cross). -See Resting State Functional MRI for processing and analysis steps EEG Using EPrime, participants hear an audio cue to switch between eyes open and eyes closed. /Volumes/L/bea_res/Tasks/EEG/7T/Resting Baseline Task text/html 2025-02-19T20:11:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:rist&rev=1739995903&do=diff Reynolds Intellectual Screening Test (RIST) Collected in 7T Behavioral Protocol, Habit Behavioral Protocol, and SPA Behavioral Visit text/html 2025-07-21T15:49:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:rsfmri&rev=1753112984&do=diff Resting State Functional MRI Data See Resting State Task for rest “task” descriptions (projector off, eyes open) Then sorted by BIDS Pre-processing Preprocessing addresses MR Motion (registration), slice timing, fieldmap unwarping (susceptibility correction) skull stripping (brain extraction) for warping (spatial normalization). text/html 2024-11-09T15:36:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:rt18&rev=1731166560&do=diff RT-18 The RT-18 is a self-report questionnaire assessing risk-taking behaviors in young people. " de Haan, L., Kuipers, E., Kuerten, Y., van Laar, M., Olivier, B., & Verster, J. C. (2011). The RT-18: a new screening tool to assess young adult risk-taking behavior. International Journal of General Medicine, 4, 575–584. text/html 2024-04-30T17:29:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:schaefer2018&rev=1714498155&do=diff Schaefer Atlas Volumetric See Yeo Lab Schaefer MNI @ github and on rhea /opt/ni_tools/atlas/schaefer2018/ (1000Parcels to 200Parcels for both 17 and 7 Network variations) 3dresample \ -inset /opt/ni_tools/atlas/schaefer2018/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_1000Parcels_17Networks_order_FSLMNI152_1mm.nii.gz \ -master $MY_FUNC_EXAMPLE \ -rmode NN \ -output schaefer-N17P1000_res-func.nii.gz text/html 2024-09-06T15:52:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:seeg_rest&rev=1725637954&do=diff sEEG Resting State text/html 2024-08-14T00:59:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:shell&rev=1723597188&do=diff Shell eg. bash (sh but “bourne” again), zsh (default for macOS), tcsh (NIH favorite) Tutorials * <https://www.tutorialspoint.com/unix/index.htm> starts super super basic but covers advance topics (via Orma) * <https://seankross.com/the-unix-workbench/command-line-basics.html> * <https://missing.csail.mit.edu/2020/shell-tools/> via Warren * <https://www.learnshell.org/> (via Amar) * AFNI's unix intro to scripting * Andy's brain blog book unix chapter includes videos * Pitt's text/html 2026-03-11T18:58:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:slipstask&rev=1773255515&do=diff Slips Task “Slips of action” is a psiturk+javascript (behavior) and python+psychopy (MR pilot, unused) port of Simplified Fabulous Fruit Game, Sanne de Wit, 2019. link active <http://rhea.wpic.upmc.edu:22362> code <https://github.com/LabNeuroCogDevel/slipstask> demo <https://labneurocogdevel.github.io/slipstask/> Serving Slips was served on heroku's free tier (amazon turk compatible) until it was discontinued. Now the slips task is served by rhea for use within the lab (UPMC i… text/html 2024-04-26T15:09:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:slurm&rev=1714144156&do=diff slurm For HPC (High performance computing) environments where there are many users who have more computation to do than the computers can handle at one time, a job queue scheduling system exists to fairly distribute and queue computation for all users. text/html 2024-03-15T16:21:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:snr&rev=1710519686&do=diff Signal to Noise Ratio (SNR) Changes in the E/I balance directly affect the signal-to-noise ratio (SNR) of local circuity, where increases in the E/I balance support the suppression of spontaneous, asynchronous, activity, in favor of evoked, synchronous firing and thus increasing SNR. The text/html 2024-06-10T13:15:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:software&rev=1718025337&do=diff LNCD Software Homegrown R, generic, and shell tools made specifically for our research * LNCDR (date_match) * lncdtools on wiki LNCD Tools (mkls for make, waitforjobs, dryrun and warn for Shell) External Here's a list of external software used for research. This is ideal reference for OAC Administered Systems. Also see text/html 2023-11-09T19:46:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:spectralevents&rev=1699559189&do=diff Spectral Event Pipeline Please refer to the LNCD Github Repository Spectral data were computed for every electrode from the 3000 – 4000 ms window of the delay epoch of the task to avoid artifact from preceding eye movements and preparation from an imminent response, and from the 1 second inter-trial fixation epoch. The spectrograms of the data were calculated from 20 to 70 Hz by convolving the signals with a complex Morlet wavelet (Qin and Shen, 2000) with 7 cycles (Shin et al. 2017). Time-f… text/html 2025-05-16T17:08:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:spm&rev=1747415320&do=diff SPM Statistical Parametric Mapping is a matlab toolbox for analyzing MR images. Many of its functions have analogs in AFNI, fsl, and nipy, as well as other MR suites. The toolbox is used for UNICORT, Neuromelanin, MRSI in HC @ 7T (scripts) (MRRC tool), and the initial implementation and inputs to PFC ROI Placement. text/html 2026-02-03T16:07:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:spmbids&rev=1770134867&do=diff SPM BIDS App A BIDS app for using SPM useful for UNICORT. A local copy_needed_only branch is on rhea:/opt/ni_tools/matlab_toolboxes/spm_bids. It's a fork (git@github.com:WillForan/SPM.git) of <https://github.com/bids-apps/SPM> Input images should be uncompressed nii files (not .nii.gz). And a BIDS root text/html 2024-11-08T16:08:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:ssh_display_forwarding&rev=1731082083&do=diff SSH Display Forwarding (X11) Secure Shell can use a local X11/Xorg server to forward applications windows. Dependencies You'll need a local X11 server. Options include * For macOS, Xquartz * For Win, MobaXterm (for UPMC managed computers, see local MobaXterm notes) or Xming * Prerequisites (Xwayland or Xorg) are likely already available when already on Linux or text/html 2024-11-08T16:08:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:ssh&rev=1731082112&do=diff Secure Shell text/html 2025-01-13T20:56:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:stq&rev=1736801776&do=diff Sleep Timing Questionnaire Used for SPA Behavioral Visit in REDCap. Also see Adolescent Sleep Wake Scale. "Monk, Timothy H.; Buysse, Daniel J.; Kennedy, Kathy S.; Potts, Jaime M.; DeGrazia, Jean M.; Miewald, Jean M. (2003). Measuring Sleep Habits Without Using a Diary: The Sleep Timing Questionnaire. Sleep, 26(2), 208–212. text/html 2025-07-14T19:29:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:strain&rev=1752521346&do=diff Stress & Adversity Inventory aka STRAIN survey. For administering instructions, see Administering STRAIN. * <https://www.uclastresslab.org/projects/strain-stress-and-adversity-inventory/> * For 7T, Dr Slavich and his lab 'own' the STRAIN so we have to go through them to obtain data. But all data should be with us now. Maria was point of contact for this, but all emails with info Maria has have been forwarded to Ashley and Amar (2024-06-04) text/html 2025-04-04T15:45:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:switchtask&rev=1743781518&do=diff 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 <https://github.com/labneurocogdevel/MMY4> written in matlab with Psychtoolbox and adapted for EEG with psycyhopy/python Bart's 2016 WPIC poster on the task: [Brain state expression and cognitive flexibility in adolescence and young-adulthood] MR See text/html 2025-12-01T18:21:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:t1t2&rev=1764613270&do=diff T1/T2 Ratio Possibly and indirect measure of myelin Calculating See <https://www.nitrc.org/projects/mrtool/> for use with SPM. On rhea for Habit Study (R37) in /Volumes/Hera/Projects/Habit/mr/myelin_mapping/T1_T2_ratio_job.m text/html 2023-09-19T14:09:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:tat2&rev=1695132595&do=diff Time-averaged T2* Acquisition * MRI data was acquired over 90 min on a 3 T Siemens Biograph mMR PET/MRI scanner. * T1 weighted magnetization-prepared rapid gradient-echo (MPRAGE) sequence * (TR, 2300 ms; echo time (TE), 2.98 ms; flip angle, 9°; inversion time (T1), 900 ms; voxel size, 1.0 × 1.0 × 1.0 mm) text/html 2026-03-11T13:48:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:templateflow&rev=1773236928&do=diff TemplateFlow <https://www.templateflow.org/> is a repository of neuroimaging Brain Templates (eg. MNI, fsLR) and a python library to pragmatically download them. This includes volumetric as well as Surface-based Analysis (cifti). You can find template flow atlases on rhea in /opt/ni_tools/templateflow/ * on Rhea (linux server) the environment variable TEMPLATEFLOW_HOME text/html 2025-10-28T19:41:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:templates&rev=1761680486&do=diff Brain Templates There are many brain templates often used as a warp target or visual underlay. Cf. “Space” (Native, MNI, TLRC). MNI152 is a popular template with multiple versions (2006, 2009a,b,c with Asymmetric and *Sym*metric versions). AFNI's 2019-03 atlases slidedeck includes a useful figure. text/html 2023-09-19T14:09:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:tidyverse&rev=1695132594&do=diff R:tidyverse/dplyr Utilities for reshaping (pivot, spread, gather) and manipulating (mutate, summarise) data.frame objects. Tidyverse includes ggplot2 as well as other packages developed for posit (makers of RStudio). text/html 2025-04-09T20:20:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:tmux&rev=1744230018&do=diff tmux tmux is a terminal multiplexer. It lets you switch easily between several programs in once terminal, detach them, and reattach them to a different terminal. In other words, you can run code in the background AND run/manage multiple terminal-based tasks simultaneously. text/html 2024-02-23T14:47:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:tutorials&rev=1708699662&do=diff Tutorials General Links * MIT's missing semester covers how to use “the command-line, use a powerful text editor, use fancy features of version control systems, and much more!” * The Shell page's tutorials section provides links for linux and the command line shell. * especially text/html 2026-02-03T16:09:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:unicort&rev=1770134966&do=diff UNICORT Unified segmentation based correction of R1 brain maps for RF transmit field inhomogeneities (UNICORT) (Weiskopf et al, 2011) is an algo available in SPM (also SPM BIDS App) to improve SNR of the MP2RAGE acquisition using an additional B1 acquisition a purely data driven approach. text/html 2025-04-14T19:14:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:uppsp&rev=1744658094&do=diff UPPS-P Impulsivity Scale In Habit Behavioral Protocol and Synaptic Pruning Adolescence (SPA), UPPS-P is collected as part of the REDCap (previously qualitrics) behavioral survey battery. The UPPS-P is a self-report questionnaire assessing personality traits that lead to impulsive-like behaviors in adults (though we use in adolescent sample). Consists of 59 items on a 4-point Likert scale, broken into five subscales: negative urgency (negurg), positive urgency (pu), sensation seeking (ss), pers… text/html 2026-03-10T14:35:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:uv&rev=1773153315&do=diff uv Python dependency/library/package manager. On rhea, setup for shared tool usage (202603): UV_CACHE_DIR=/opt/ni_tools/python/uv/cache UV_TOOL_DIR=/opt/ni_tools/python/uv/tool UV_TOOL_BIN_DIR=/opt/ni_tools/python/uv/bin text/html 2025-04-30T20:20:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:vgs&rev=1746044414&do=diff Visually Guided Saccade Task * Originally in EPrime, see /Volumes/L/bea_res/Tasks/Behavorial/vgs-beakid * For Habit EEG Protocol and SPA EEG, we use 7T EEG's vgs_ant.py (Psychopy) part of Memory Guided Saccade (MGS) Task text/html 2025-10-07T18:35:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:vim&rev=1759862112&do=diff Vim vim is a modal editor (improving on vi). It can run without graphics, is ubiquitous, powerful, and efficient but is an acquired skill. MIT's “missing semester” has an excellent summary of vim functions video and notes. Vim’s design is based on the idea that a lot of programmer time is spent reading, navigating, and making small edits, as opposed to writing long streams of text. For this reason, Vim has multiple operating modes. text/html 2025-07-21T17:02:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:whoqol-bref&rev=1753117337&do=diff World Health Organization Quality of Life (WHOQOL-BREF) Described on <https://www.who.int/tools/whoqol/whoqol-bref> (manual) Also see the National Data Archive data dictionary <https://nda.nih.gov/data-structure/whoqol01> Collected in Synaptic Pruning Adolescence (SPA) Habit Study (R37) and 7T Behavioral Protocol text/html 2023-11-14T14:42:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:wiki&rev=1699972942&do=diff Wiki (tool) Wiki's enable collaborative knowledge management and provides an information system. From Luo & Cea, 2020 " A wiki is ... created quickly, incrementally, and collaboratively, and they can be shared with and edited by peers. " And from Nagan 2020: " the lab wiki is the central resource for maintaining and passing on research group knowledge. text/html 2023-12-28T00:19:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.lncd.pitt.edu/wiki/doku.php?id=tools:wormhole&rev=1703722770&do=diff Magic Wormhole Magic Wormhole is a tool to easy way to send data (a file or a directory) between a local computer and rhea. You need shell access on both the sender and receiver, but the computers can be on separate networks each behind their own firewalls.