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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ERPLAB Resource Report Resource Website 100+ mentions |
ERPLAB (RRID:SCR_009574) | ERPLAB | software application, software resource, data processing software, data analysis software | A set of open source, freely available Matlab routines for analyzing Event Related Potential (ERP) data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH. | anova, eeg, meg, electrocorticography, event related potential, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Bioelectromagnetism Matlab Toolbox has parent organization: University of California at Davis; California; USA |
NIMH | GNU General Public License | nlx_155754 | http://www.nitrc.org/projects/erplab | SCR_009574 | ERPLAB Toolbox | 2026-07-27 09:33:21 | 428 | |||||
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BRAINSDemonWarp Resource Report Resource Website 1+ mentions |
BRAINSDemonWarp (RRID:SCR_009524) | BRAINSDemonWarp | image analysis software, software resource, software application, registration software, data processing software | A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: University of Iowa; Iowa; USA |
NINDS NS050568; NINDS NS40068; NIMH MH31593; NIMH MH40856 |
nlx_155700 | http://www.nitrc.org/projects/brainsdemonwarp | SCR_009524 | 2026-07-27 09:33:20 | 1 | |||||||
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NKI-RS Multiband Imaging Test-Retest Pilot Dataset Resource Report Resource Website 1+ mentions |
NKI-RS Multiband Imaging Test-Retest Pilot Dataset (RRID:SCR_010460) | NKI-RS Multiband Test-Retest Pilot Dataset | data or information resource, data set | A test-retest dataset to assess the reliability of multiband resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI) scans prior to launch of the Enhanced Nathan Kline Institute - Rockland Sample (NKI-RS). The dataset is primarily composed of individuals from the initial NKI-RS - for these individuals psychiatric assessment information is available and included (participants were not excluded due to history of illness. In addition to R-fMRI and DTI, they included: 1) simple visual checkerboard stimulation fMRI scans to allow for assessment of traditional fMRI data quality metrics (e.g., contrast-to-noise ratio), 2) breath holding data to enable assessment of regional differences in vascular responsiveness, and 3) eye movement calibration scans to enable the assessment of eye-movement related artifacts which may be particularly troublesome for multiband sequences since several slices are acquired simultaneously. | demographic, multiband imaging, resting state fmri, diffusion tensor imaging, breath hold scan, eye movement calibration scan, visual stimulation scan, brain development, maturation, young human, late adult human, child, adolescent, adult human, image collection, pediatric, geriatric, behavior, cognitive, phentoyping, neuroimaging, dicom, nifti, multiband echo planar imaging, multiband resting state fmri, multiband diffusion tensor imaging, psychiatric assessment |
is related to: NKI/Rockland Sample is related to: NKI-RS Enhanced Sample has parent organization: 1000 Functional Connectomes Project has parent organization: Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; Child Mind Institute 1FDN2012-1; NIMH R01MH094639-01; NIMH R01MH081218; NIMH R01MH083246; NIMH R21MH084126 |
Creative Commons Attribution-NonCommercial License | nlx_157648 | SCR_010460 | Enhanced Nathan Kline Institute-Rockland Sample Multiband Imaging Test-Retest Pilot Dataset, Enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) Multiband Imaging Test-Retest Pilot Dataset | 2026-07-27 09:33:38 | 1 | |||||
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NKI-RS Enhanced Sample Resource Report Resource Website 50+ mentions |
NKI-RS Enhanced Sample (RRID:SCR_010461) | Enhanced NKI-RS | data or information resource, data set | Dataset of 1000 characterized community-ascertained participants using state-of-the-art multiband imaging-based resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI), genetics, and a deep phenotyping protocol from a large cross-sectional sample of brain development, maturation and aging (ages 6 - 85 yrs). The Center for Magnetic Resonance Research (CMRR), University of Minnesota, provided the NKI-RS effort with the latest version of the Multiband EPI sequence (Xu et al. 2012) and associated image reconstruction algorithms, enabling the acquisition of state-of-the-art imaging datasets for this large-scale imaging effort. The enhanced NKI-RS expands upon the phenotypic protocol of the original NKI-RS and captures a broad range of behavioral and cognitive phenomenology relevant to psychiatric health and illness. The validity and value of assessments were evaluated by consulting leaders in the field of psychiatric phenotyping. | demographic, multiband imaging, resting state fmri, diffusion tensor imaging, breath hold scan, eye movement calibration scan, visual stimulation scan, brain development, maturation, young human, late adult human, child, adolescent, adult human, image collection, pediatric, geriatric, behavior, cognitive, phentoyping, neuroimaging, dicom, nifti, multiband echo planar imaging, multiband resting state fmri, multiband diffusion tensor imaging, lifespan, physiological assessment, psychological assessment, genetic |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NKI/Rockland Sample is related to: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is related to: Mind Research Network - COINS is related to: NIMH Repository and Genomics Resources has parent organization: Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; Child Mind Institute 1FDN2012-1; NIMH R01MH094639-01; NIMH R01MH081218; NIMH R01MH083246; NIMH R21MH084126 |
Public, Data Usage Agreement | nlx_157649 | SCR_010461 | Enhanced Nathan Kline Institute - Rockland Sample | 2026-07-27 09:33:44 | 97 | |||||
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histoCAT Resource Report Resource Website 1+ mentions |
histoCAT (RRID:SCR_026499) | source code, software resource, software toolkit | Software package to visualize and analyse multiplexed image cytometry data interactively. | visualize and analyse multiplexed image, image cytometry data, interactively | NIA R01AG066027; NIMH U19MH114830 |
PMID:28783155 | Free, Available for download, Freely available | SCR_026499 | Histology Topography Cytometry Analysis Toolbox | 2026-07-27 09:37:39 | 2 | ||||||||
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Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | source code, software resource, software toolkit | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-07-27 09:37:40 | 1 | |||||||||
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Ecosystem for Multi-modal Brain-behavior Experimentation and Research Resource Report Resource Website 1+ mentions |
Ecosystem for Multi-modal Brain-behavior Experimentation and Research (RRID:SCR_026700) | EMBER | service resource, storage service resource, data repository, data or information resource | BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program. | data archive, multi-modal neurophysiological data, behavioral data, Brain Behavior Quantification and Synchronization (BBQS) Program, |
is related to: Distributed Archives for Neurophysiology Data Integration is related to: Brain Observatory Storage Service and Database (BossDB) has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
NIMH R24MH136632; NIDA R24DA064430 |
Free, Freely available | SCR_026700 | , Ecosystem for Multi-modal Brain-behavior Experimentation and Research (EMBER), EMBER Archive | 2026-07-27 09:37:42 | 6 | |||||||
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WASP Resource Report Resource Website 1+ mentions |
WASP (RRID:SCR_025497) | software resource, source code, software toolkit | Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery. | molecular QTLs discovery, unbiased allele-specific read mapping and discovery, molecular QTLs, unbiased allele-specific read, mapping and discovery, | Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG006123; NIMH MH101825; NIGMS GM007197; NSF |
PMID:26366987 | Free, Available for download, Freely available, | SCR_025497 | 2026-07-27 09:37:25 | 3 | |||||||||
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NIMP Analytics Resource Report Resource Website |
NIMP Analytics (RRID:SCR_028218) | NIMP | web service, project portal, software resource, portal, data access protocol, data or information resource | Neuroanatomy-anchored Information Management Platform for collaborative BICAN data generation developed by UTHealth Houston. Serves as metadata tracking engine to support generation, management, and sharing of brain research data. Integrates data production pipelines across brain banks, laboratories, sequencing centers, and data archives. Platform enables integrative and collaborative, consortium-scale FAIR data generation within the BICAN project. Platform is designed to manage complex dataset, including tissue samples and sequencing data, through Specimen Portal and Sequence Library Portal. Portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting. | FAIR, BICAN, CUBIE, Sample Tracking, Data Ecosystem, Brain Tissue, Multi-Omics Profiling Expression Database, neuroanatomy, collaborative BICAN data generation, | is organization facet of: BRAIN Initiative Cell Atlas Network | NIMH U24MH130988 | PMID:41573954 | Free, Freely available, | https://brain-specimenportal.org | SCR_028218 | Neuroanatomy-Anchored Information Management Platform (NIMP) | 2026-07-27 09:38:06 | 0 | |||||
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dreamlet Resource Report Resource Website |
dreamlet (RRID:SCR_028168) | source code, software resource, software toolkit | Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights. | Perform differential expression analysis, multi-sample single cell datasets, linear mixed models, precision weights, | NIA R01AG067025; NIA R01AG065582; NIA R01AG050986; NIA P30AG066514; NIMH R01MH109677; NIMH R01MH125246; NIMH RF1MH128970; NIMH U01MH116442; NINDS U01NS125580 |
PMID:36993704 | Free, Available for download, Freely available | SCR_028168 | 2026-07-27 09:38:07 | 0 | |||||||||
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PERI: Prospective Evaluation of Reproductive aging Indicators Resource Report Resource Website |
PERI: Prospective Evaluation of Reproductive aging Indicators (RRID:SCR_028698) | software resource, source code, software toolkit | Software R code to apply Stages of Reproductive Aging Workshop + 10 stages to prospectively collected vaginal bleeding data among a cohort of Black women aged 40–55 years. Used to apply STRAW+10 stages to prospectively tracked menstrual bleeding data in a longitudinal cohort study of perimenopausal women. | Stages of Reproductive Aging Workshop, perimenopausal women, prospectively tracked menstrual bleeding data, STRAW+ 10 stages, prospectively collected vaginal bleeding data, | NIMH R01MH128244; NIMH F32MH134528; NINDS T32NS096050 |
PMID:41576711 | Free, Available for download, Freely available | SCR_028698 | 2026-07-27 09:38:15 | 0 | |||||||||
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Multimodal Surface Matching Resource Report Resource Website |
Multimodal Surface Matching (RRID:SCR_024929) | MSM | image analysis software, software resource, software application, registration software, data processing software | Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity. | registering cortical surfaces, brain architecture, function and connectivity, | is a plug in for: FSL | NIMH 1U54MH091657; NIMH F30 MH097312 |
PMID:24939340 | Free, Freely available | SCR_024929 | MSM:Multimodal Surface Matching | 2026-07-27 09:37:19 | 0 | ||||||
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FMRIB’s Integrated Registration and Segmentation Tool Resource Report Resource Website 1+ mentions |
FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) | FIRST | data analysis software, image analysis software, software resource, software application, registration software, data processing software, segmentation software | Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences. | Functional Magnetic Resonance Imaging of the Brain, segmentation, registration, volumetric segmentation, performing vertex analysis, |
is related to: Multimodal Image Segmentation Tool is a plug in for: FSL |
NCRR P41 RR14075; NINDS R01 NS052585; NCRR R01 RR16594; NIMH K08 MH01573; NIMH K01 MH01798; NIDA R01 DA017905 |
PMID:21352927 | Free, Freely available | SCR_024921 | , Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool | 2026-07-27 09:37:15 | 2 | ||||||
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Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | 2026-07-27 09:31:42 | 3 | |||||||
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Neurophysiology Imaging Facility Resource Report Resource Website |
Neurophysiology Imaging Facility (RRID:SCR_004080) | NIF | access service resource, core facility, service resource | Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates. | mri, fmri, neuroimaging, neurophysiology, brain | has parent organization: National Institute of Mental Health | NIMH ; NINDS ; NEI |
nlx_158530 | SCR_004080 | Neurophysiology Imaging Facility (NIF) | 2026-07-27 09:31:56 | 0 | |||||||
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NKI/Rockland Sample Resource Report Resource Website 10+ mentions |
NKI/Rockland Sample (RRID:SCR_009435) | data or information resource, data set | A phenotypically rich neuroimaging sample, consisting of data obtained from individuals between the ages of 4 and 85 years-old. All individuals included in the sample undergo semi-structured diagnostic psychiatric interviews, and complete a battery of psychiatric, cognitive and behavioral assessments in order to provide comprehensive phenotypic information for the purpose of exploring brain / behavior relationships. | image collection, young human, late adult human, neuroimaging, phenotype, fmri, dti, mprage, t2, psychiatric assessment, cognitive assessment, behavioral assessment, resting state fmri, dicom, nifti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Rockland Download Link Script is related to: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is related to: NKI-RS Enhanced Sample has parent organization: 1000 Functional Connectomes Project |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; NKI Center for Advanced Brain Imaging CABI ; the Brain Research Foundation Chicago ; the Stavros Niarchos Foundation ; NIMH P50 MH086385-S1 |
Creative Commons Attribution-NonCommercial License | nlx_155538 | http://www.nitrc.org/projects/dl_dataset | SCR_009435 | Nathan Kline Institute / Rockland Sample, NKI Rockland Sample, Nathan Kline Institute (NKI) / Rockland Sample | 2026-07-27 09:33:19 | 17 | |||||
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CellTax vignette Resource Report Resource Website 1+ mentions |
CellTax vignette (RRID:SCR_017000) | data or information resource, data set | Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing. | data, classification, cell, type, mammalian, brain, cellular, taxonomy, mouse, visual, cortex, gene, expression, pattern, cortical, region |
is related to: Allen Brain Atlas API is related to: Allen Mouse Brain Reference Atlas is related to: Allen Cell Types Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science ; NEI R01 EY023173; NIMH U01 MH105982 |
PMID:26727548 | Free, Public | SCR_017000 | Cellular Taxonomy of the Mouse Visual Cortex, Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science | 2026-07-27 09:35:28 | 3 | |||||||
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HED Tags Resource Report Resource Website 1+ mentions |
HED Tags (RRID:SCR_014074) | HED | narrative resource, data or information resource, standard specification | Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging. | Data, structure, standard, EEG, brain, imaging, comma, separated, path, string, analysis, MEG, fNIRS, multimodal, ECG, EMG, GSR, behavioral, BRAIN Initiative |
is used by: NIMH Data Archive is used by: HeadIT is used by: OpenNeuro is recommended by: BRAIN Initiative has parent organization: University of California at San Diego; California; USA |
Swartz Foundation ; Army Research Laboratory Cooperative Agreement ; NIMH R01MH084819; NINDS R01 NS047293 |
PMID:27799907 | Free, Freely available | SCR_017630 | SCR_014074 | Hierarchical Event Descriptor Tags, Hierarchical Event Descriptor, HED, HED tags | 2026-07-27 09:34:32 | 7 | |||||
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WINGS Resource Report Resource Website 10+ mentions |
WINGS (RRID:SCR_013997) | software application, systems interoperability software, data management software, software resource | A software application which assists scientists with designing computational experiments. WINGS is a semantic workflow system which incorporates semantic constraints about datasets and workflow components into its workflow representations. The workflow system has an open modular design and can be easily integrated with other existing workflow systems and execution frameworks to extend them with semantic reasoning capabilities. WINGS also allows users to express high-level descriptions of their analysis goals, and assists them by automatically and systematically generating possible workflows that are consistent with that request. In cases where privacy or off-line use are important, WINGS can submit workflows in a scripted format for execution in the local host. It uses Pegasus or OODT as the execution engine for large-scale distributed workflow execution. | semantic workflow system, software application, computational experiment, computational experiment design, data management software |
is listed by: Connected Researchers is related to: Connected Researchers |
NSF CCF-0725332; NSF IIS-0917328; NSF IIS-0948429; NSF CSR-0615412; NIMH U24 MH068457; Defense Advanced Research Projects Agency HR0011-07-C-0060; Air Force Research Laboratory FA8750-06-C-0210 |
Free, Public | SCR_013997 | Workflow Instance Generation and Specialization | 2026-07-27 09:34:31 | 27 | ||||||||
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JWatcher Resource Report Resource Website 10+ mentions |
JWatcher (RRID:SCR_017595) | data analysis software, software resource, data acquisition software, software application, data processing software, data analytics software | Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer. | Quantitative, analysis, behavior, theoretical, problem, action, scored, human, observer |
has parent organization: University of California at Los Angeles; California; USA has parent organization: Macquarie University; Sydney; Australia |
NIMH R21 MH065226; Australian Research Council ; Macquarie University |
Free, Available for download, Freely available | SCR_017595 | 2026-07-27 09:35:32 | 49 |
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