NITRC Community News

mri_reface 0.3.5

Christopher Schwarz — Fri, 13 Dec 2024 2:45:11 GMT

Today we have released mri_reface 0.3.5. Major changes include support for ASL and PD MRI, support for full-dynamic and "early" PET, support for NAV4594 and PI2620 PET, a build for use on ARM "Silicon" Macs, better recognition of image types from BIDS names, options to tweak behavior of multi-volume inputs, options to tweak the brain/face boundary location, and many other requested fixes and enhancements. It is recommended to update to this release, which can be used as an "in place" upgrade.

NBCD - Coming January 2025!

Angie Laird — Thu, 21 Nov 2024 4:25:04 GMT

Coming January 2025! We are excited to announce the launch of the NIH Brain Development Cohorts (NBDC) Data Sharing Platform. This new data ecosystem will host and facilitate access to data from both the Adolescent Brain Cognitive DevelopmentSM (ABCD) Study and the HEALthy Brain and Child Development (HBCD) Study.

The NBDC platform will offer a range of functionalities:

Scalable Data Integration: Seamlessly manage large volumes of data, including neuroimaging and genomics data

Customized Query Tools: Easily navigate data dictionaries to find the variables you need for your research goals

Streamlined Data Use Certification (DUC) Workflows: Choose individual or investigator-led group DUC. Visit the NBDC platform to learn more: https://nbdc-duconly.lassoinformatics.com. Researchers with an active DUC from the NIMH Data Archive will need to obtain a new DUC

Responsible Use Training: Complete training on responsible and ethical data and biospecimen use prior to data access approval

ABCD data users: The ABCD 6.0 data release includes cumulative data from baseline through the six-year follow-up visit, with data from about 75% of participants at that timepoint. ABCD data from prior data releases will be transferred from the NIMH Data Archive to the NBDC platform.

HBCD data users: The inaugural HBCD data release includes data from over 1100 pregnant participants during the prenatal period. For over half of these participants, follow-up data from their babies are also included.

For detailed information about the NBDC studies, please visit the ABCD study® wiki at wiki.abcdstudy.org or the HBCD Study data sharing page at https://hbcdstudy.org/data-sharing

Questions? Email: nbdc@mail.nih.gov

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.