NITRC Community News

NeuroDOT (v1.4) and NeuroDOT_py (v1.0.0) Releases

Emma Speh — Wed, 23 Oct 2024 9:09:53 GMT

We are excited to announce the latest NeuroDOT (v1.4) & NeuroDOT_py (v1.0.0) releases on GitHub and PyPi! The Matlab release features improvements to format compatibility with NIfTI, SNIRF, and LUMO, a new tutorial for participant-specific head modeling, and an interactive user-interface for rendering data on a mesh. For NeuroDOT_py, a Sphinx-based documentation site is now available in addition to the toolbox being available via PyPi. This release was made possible thanks to the efforts of the NeuroDOT Development Team and the Brain Light Lab at WashU.

Become a registered NeuroDOT user to receive development updates, news about workshops, and individual help from the NeuroDOT team: https://tinyurl.com/NeuroDOT

The advancements represented in this update were supported by the National Institute of Neurological Disorders and Stroke (NINDS) of The National Institutes of Health under Award Number U24NS136402. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Release of Brainstem Navigator v1.0

Marta Bianciardi — Wed, 16 Oct 2024 2:06:06 GMT

We are pleased to announce the release of the Brainstem Navigator v1.0, which you can download here:
https://www.nitrc.org/projects/brainstemnavig/

NEW FEATURE: a tutorial of coregistration scripts able to align the brainstem nuclei atlas to structural, diffusion and functional MRI of living humans!

Same atlas labels and templates as in the Brainstem Navigator v0.9, i.e.:
- 31 brainstem nuclei labels (8 medial/23 bilateral), and 11 brainstem subnuclei labels (bilateral) for a total of 76 brainstem nuclei labels;
- 3 diencephalic nuclei labels (bilateral), and 2 diencephalic subnuclei labels (bilateral) for a total of 10 diencephalic labels;
- MRI templates of the brainstem and diencephalon.

GenMIND dataset v1.0 released

Spandana Chintapalli — Tue, 08 Oct 2024 3:26:09 GMT

genmind_dataset.csv contaisn 18000 synthetic samples with demographic and brain ROI volume information.

PESTICA & SLOMOCO release on GitHub

Wanyong Shin — Fri, 27 Sep 2024 3:21:57 GMT

Dear PESTICA & SLOMOCO users,

PESTICA & SLOMOCO software package development platforms are moved to GitHub. Also, a SLOMOCO package was initially included in a PESTICA package, but SLOMOCO is the independent software and project now. They are plugged to each other in a pipeline, but can be used independently. Please go to the links below to find the latest version of PESTICA and SLOMOCO.

PESTICA project
https://github.com/wanyongshinccf/PESTICA

SLOMOCO project
https://github.com/wanyongshinccf/SLOMOCO

NITRC v2.1.70 released

NITRC Moderator — Tue, 24 Sep 2024 8:53:23 GMT

We are pleased to announce the release of NITRC v2.1.70. This release includes several small but useful features. Of special note is GitLab integration, allowing projects to link to GitLab repositories and pull certain data and release information into NITRC.

Release notes can be found at https://www.nitrc.org/plugins/mwiki/index.php?title=nitrc:NITRC_Release_Notes#NITRC-R_Release_v2.1.70-0_-_09.2F23.2F2024

NBS-Predict v1.0.0-beta.13 released

Emin Serin — Wed, 11 Sep 2024 12:31:06 GMT

In this version, we fixed random seed errors that might happen in the newer versions of MATLAB (R2014a or newer)!

UNC-BCP 4D Infant Brain Volumetric Atlas Ver2.0.0 Released!

Liangjun Chen — Wed, 04 Sep 2024 8:46:28 GMT

In the Version 2.0, the atlas was updated in the following details:
1.We extended the atlas to 60 months by providing the atlases of 36-month, 48-month, and 60-month.
2.The segmentation maps were rebuilt by applying the iBEAT V2.0 on T1w and T2w templates, instead of using the original segmentation maps achieved through the atlas building procedures, to provide more accurate tissue segmentation maps.
3.The newly built segmentation maps were further manually revised to keep the consistency with the parcellation maps.
4.Some errors in the header files were fixed.

Medical Image De-Identification Benchmark (MIDI-B) Challenge

David Kennedy — Tue, 18 Jun 2024 3:16:55 GMT

The National Cancer Institute (NCI) is excited to announce the launch of the Medical Image De-Identification Benchmark (MIDI-B) Challenge (https://www.synapse.org/Synapse:syn53065760/wiki/625274) with the goal of assessing rule-based DICOM de-identification (deID) algorithms using a large and diverse set of standardized clinical images with synthetic identifiers. Automated image de-identification methods that reserve the research utility of the data are desirable.

To learn more, please visit the website: MIDI-B De-identification - syn53065760 - Wiki (synapse.org). (https://www.synapse.org/Synapse:syn53065760/wiki/627881)

Participation by teams from industry and academia is encouraged. Please forward this information to interested colleagues.

XNAT Central Migration to NITRC-IR

NITRC Moderator — Thu, 13 Jun 2024 1:38:17 GMT

XNAT Central, a long-standing data sharing platform, has reached its end of life. As a result, NITRC-IR has adopted major projects from XNAT Central. Two exemplary high-profile datasets migrating are:

Open Access Series of Imaging Studies (OASIS)

This multimodal dataset from the Knight ADRC at Washington University includes cross-sectional and longitudinal neuroimaging, clinical, cognitive, and biomarker data for normal aging and Alzheimer's disease. It includes data for OASIS-Cross-sectional and OASIS-Longitudinal studies. It has been widely used for analyses, atlas development, and segmentation algorithms.

Northwestern University Schizophrenia Data and Software Tool (NUSDAST)

NUSDAST is an NIH-funded data sharing project to stimulate new research in schizophrenia that contains neuroimaging, cognitive, clinical, and genetic data from over 450 subjects with schizophrenia, most with 2-year longitudinal follow-up.

Find these and other datasets at https://www.nitrc.org/ir/

Healthy Brain Network Data Release 11.0

David Kennedy — Thu, 06 Jun 2024 1:07:14 GMT

Dear Colleagues,

We are happy to announce Release 11 of the Healthy Brain Network (HBN) dataset. Leveraging a community-referred recruitment model, HBN is a large transdiagnostic open science database. It includes phenotypic and behavioral monitoring, MRI, EEG, eye tracking, and biological data. Please visit the HBN Scientific Data Portal (https://fcon_1000.projects.nitrc.org/indi/cmi_healthy_brain_network/?utm_medium=email&utm_source=oneoff&utm_campaign=new-indi-release-2024-06&utm_content=cmi_healthy_brain_network) for detailed information about the initiative and the dataset. As always, you can email us (CMIDataUsage@childmind.org) for user support and discussion.

Regards,

The HBN and DISK Teams

RELEASED DATA CUTOFF DATE: 11/23/2022

Release Contents

Phenotypic data
New datasets: n=728
Total datasets: n=4867
Neuroimaging data
EEG and eye tracking
New datasets: n=572
Total datasets: n=4142
Multi-modal MRI
New datasets: n=459
Total datasets: n=3905
Website and Documentation Update

April 2024:

The HBN website and documentation has undergone a significant update and improvement, which includes:

A new and up-to-date assessment list, which contains extensive information about all HBN instruments and tasks
Updates to our data dictionaries
Updates to the HBN support forum
Data Additions

November 2022:

Phenotypic Data:
The CoRonavIruS Health Impact Survey (CRISIS) data for Healthy Brain Network participants have been added into the release (only on LORIS). Data was collected at two time points: April 2020 and February 2021. For more information about CRISIS please visit the Crisis Survey.
Data Fixes

November 2022:

Phenotypic Data:
Removed duplicated rows for the following assessments:
Child Behavior Checklist – Teacher Report Form (TRF)
Daily Meds
Fixed assessments on COINS that had duplicated participants due to upload errors into the COINS platform. Assessments that may have experienced this error are:
CFS
GARS
GRIT
GSE
IUQ_P
IUQ_SR
KSADS
PBS
Peds_Migraine
PMHS
PreInt_Lang
RemoteTask
TBI
WAIS
WISC
April 2024:

Phenotypic Data:
Separated Diagnosis_KSADS into three instruments: Diagnosis_KSADS_T, Diagnosis_KSADS_P, Diagnosis_KSADS_D (teen, parent, clinician)
Removed duplicated participants from HBN_R4_Pheno, HBN_R7_Pheno, HBN_R8_Pheno, HBN_R10_Pheno
Removed the following duplicate instruments from LORIS
AUDIT (duplicate of Audit)
Renamed the following instruments on LORIS:
ARI_S > ARI_SR
Bia_final > BIA
FFQ_final > FFQ
temp_disc_final > Temp_Disc_Final
Indicated in SRS_Pre data dictionary that the T-Score standardization is based on a sample of children < 4.5 years old and thus might be inaccurate for children above this age
Fixed the coding of the following data dictionaries:
CPIC
DTS
GRIT
ICU_P
ICU_SR
SCQ
SDQ
SRS
SRS_Pre
STAI
Other Fixes and Updates:

As of April 2024, we are reviewing data overlaps between the following instruments on LORIS:
ACE_Flanker and ACE_FLANKER
TRF_P and TRF_Pre
CELF_Meta and CELF5_Meta
PhenX_School and PhenX_SchoolRisk
PreInt_FamHx and PreInt_FamHx_RDC
While all EEG participants have age and sex data available, not all EEG participants have phenotypic assessment data available at this time. Those data items will be released in Release 12. Find links to imaging data downloads on our data portal.