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DCAN-Labs

35 indexed repositories · View on GitHub

abcd-hcp-pipeline
bids application for processing functional MRI data, robust to scanner, acquisition and age variability.

Python · 59 stars
functional-random-forest
Functional Analysis with Random Forests

MATLAB · 22 stars
compare_matrices_to_assign_networks

MATLAB · 15 stars
cifti-connectivity
Script to generate correlation matrices from BOLD dense or parcellated time series data.

MATLAB · 13 stars
BIBSnet
This BIDS App provides the utility of creating a nnU-Net anatomical MRI segmentation and mask with a infant brain trained model. It can ...

Python · 13 stars
dcan_bold_processing
functional connectivity preprocessing for resting state fMRI outputs of the dcan-fmri-pipelines

MATLAB · 9 stars
file-mapper
An easy tool to copy/move/symlink files from one directory to the other!

Python · 8 stars
infant-abcd-bids-pipeline
Human infant pipeline, based on abcd-hcp-pipeline, to process fMRI data.

Python · 8 stars
DCAN-HCP
The DCAN Lab's version of the minimal preprocessing pipeline for the Human Connectome Project

Shell · 7 stars
nhp-abcd-bids-pipeline
Non-human primate (i.e., macaque) pipeline, based on abcd-hcp-pipeline, to process fMRI data.

Python · 6 stars
movement_regressors_power_plots
Correction of respiratory artifacts in MRI head motion estimates

MATLAB · 5 stars
abcd-bids-tfmri-pipeline
Pipeline to complete within-run and between-runs analyses of task-based fMRI dense timeseries data. This tool works with data that were m...

Python · 4 stars
dcan-macaque-pipeline
The actual pipeline code, based on hcp, for non-human-primates - sp macaques.

Shell · 3 stars
cdni-brain
readthedocs for CDNI collaborators and members

3 stars
CABINET
CABINET is a utility that standardizes subsequent container execution. Emphasizing reproducibility, users can share JSONs to exactly repl...

Python · 1 star
abcd-hcp-pipeline_audit

Python · 1 star
SLURM_wrappers
Bash and Python wrappers for SLURM that streamline HPC job submission, AWS S3 data transfers, and disk-based workflows; adaptable to any ...

Shell · 1 star
QSIPREP_HBCD_QC
Tool to make QC images for HBCD's QSIPREP Output

Python · 1 star
hbcd_qmri_postproc

Python · 1 star
OSPREY_BIDS
Houses the Dockerfile used to compile OSPREY

Python · 1 star
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206 open issues indexed

Analyses_v2 timecourses overwriting output csv (I believe) Open

bug invalid medium priority

DCAN-Labs/abcd-hcp-pipeline#55 · 2 comments · 0 reactions · 3 assignees · Indexed Sep 15, 2026
Possible ants bracket expansion bug Open

bug

DCAN-Labs/abcd-hcp-pipeline#96 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
About the template used in ABCD Open

DCAN-Labs/abcd-hcp-pipeline#124 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
question regarding the functional connectivity matrix of ABCD two-year follow-up rsfMRI data Open

DCAN-Labs/abcd-hcp-pipeline#125 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Integrate documentation on derivative outputs into readthedocs Open

enhancement

DCAN-Labs/abcd-hcp-pipeline#132 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Minor updates/clean up per NMIND team recommendation Open

enhancement

DCAN-Labs/abcd-hcp-pipeline#134 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
ABCC Collection - pconn.nii ROI names. Open

enhancement

DCAN-Labs/abcd-hcp-pipeline#139 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Quality check output from Segmentation pipeline Open

enhancement

DCAN-Labs/BIBSnet#21 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Test possible bugs with --overwrite flag & possibly default to clearing old outputs until this is resolved Open

bug

DCAN-Labs/BIBSnet#44 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Make aseg-derived mask only once Open

enhancement

DCAN-Labs/BIBSnet#48 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
settings_comparematrices should have an otherwise Open

DCAN-Labs/compare_matrices_to_assign_networks#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
T2 images rotated during T2 to T1 alignment in preBIBSNet Open

bug

DCAN-Labs/BIBSnet#50 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
List required packages and links to download them in the readme Open

DCAN-Labs/compare_matrices_to_assign_networks#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add fslorient to check orientation and either exit with error if orientation/header info is non-compatible with BIBSNet utilities or use fslorient2std to make compatible Open

enhancement

DCAN-Labs/BIBSnet#98 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
do not find pre-made template file Open

DCAN-Labs/compare_matrices_to_assign_networks#6 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
FYI: submitted to be included in the bids-apps registry Open

DCAN-Labs/BIBSnet#109 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
tutorial issues Open

DCAN-Labs/compare_matrices_to_assign_networks#7 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Figure out more elegant solution for handling files used in multiple stages of the pipeline Open

enhancement

DCAN-Labs/BIBSnet#119 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use GitHub Actions to automatically update version number in Dockerfile Open

enhancement good first issue

DCAN-Labs/BIBSnet#131 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Include input tab/comma separated value files Open

DCAN-Labs/nibabies-paper-code#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove flags not included in ReadTheDocs from usage Open

enhancement

DCAN-Labs/BIBSnet#136 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Output nnU-Net inference/prediction routines as derivatives Open

enhancement

DCAN-Labs/BIBSnet#139 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Deal with WARNING messages output at top of logs in some way so that they don't confuse users Open

enhancement

DCAN-Labs/BIBSnet#140 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 15, 2026
add input dataset example to documentation Open

DCAN-Labs/Seg-Model-Creation-GUI#1 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 15, 2026
Use SynthStrip-derived brainmask instead of current aseg-derived brainmask Open

enhancement

DCAN-Labs/BIBSnet#142 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
implement an option/argument for an additional custom label file Open

DCAN-Labs/Seg-Model-Creation-GUI#2 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
RuntimeError: CUDA error: no kernel image is available for execution on the device Open

question

DCAN-Labs/BIBSnet#149 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
use sklearn stratify to implement automated stratification Open

DCAN-Labs/Seg-Model-Creation-GUI#3 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Potentially use structural similarity index instead of eta squared to choose optimal preBIBSNet workflow Open

bug

DCAN-Labs/BIBSnet#150 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
implement tabs system to open multiple instances of the program Open

DCAN-Labs/Seg-Model-Creation-GUI#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
User flag on docker Open

enhancement

DCAN-Labs/BIBSnet#155 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
implement ability to run multiple tasks at the same time Open

DCAN-Labs/Seg-Model-Creation-GUI#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Issue running BIBSnet when accessing files from a mounted server Open

question

DCAN-Labs/BIBSnet#165 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
adapt source code for new containerization abilities Open

enhancement

DCAN-Labs/Seg-Model-Creation-GUI#8 · 1 comment · 0 reactions · 3 assignees · Indexed Sep 15, 2026
optional Output of label probability maps by nnUnet Open

enhancement

DCAN-Labs/BIBSnet#166 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remove input fields and reliance on SynthSeg and dcan-nn-unet repo specific paths from GUI Open

DCAN-Labs/Seg-Model-Creation-GUI#11 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
Rescaling segmentation issue causing failures in ~15% of cases Open

bug

DCAN-Labs/BIBSnet#167 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
output any intermediate files originally created by GUI code into a separate work dir Open

DCAN-Labs/Seg-Model-Creation-GUI#12 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create new field for specifying a particular MSI account for job submission Open

DCAN-Labs/Seg-Model-Creation-GUI#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update NVIDIA CUDA PyTorch Driver in docker container to support sm_90 Open

enhancement

DCAN-Labs/BIBSnet#171 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
RADIOLOGICAL Orientation Required Open

enhancement

DCAN-Labs/BIBSnet#172 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
model 545 vs 547 -a report from the Autism Phenome Project on model differences Open

DCAN-Labs/BIBSnet#175 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
MIssing image in bugs page Open

bug

DCAN-Labs/BrainSwipes#14 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Brain scans stop loading after x swipes (happens hbcd maybe all private). Open

bug

DCAN-Labs/BrainSwipes#15 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add test tab to all admin accounts Open

enhancement

DCAN-Labs/BrainSwipes#16 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create a simple visual explanation of NIFTI and CIFTI header information Open

DCAN-Labs/cdni-brain#61 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add Simple Datalad Usage Open

DCAN-Labs/cdni-brain#62 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve database/update-samples from s3 Open

enhancement

DCAN-Labs/BrainSwipes#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add ORCID ID information Open

DCAN-Labs/cdni-brain#113 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Missing study buttons on reload Open

bug

DCAN-Labs/BrainSwipes#18 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

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