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neuropoly

7 indexed repositories · View on GitHub

totalspineseg
Robust Segmentation and Labeling of Vertebrae, Intervertebral Discs, Spinal Cord, and Spinal Canal in MRI Images Using nnU-Net and Iterat...

Python · 117 stars
intranet.neuro.polymtl.ca
NeuroPoly's lab manual

HTML · 8 stars
SmaugLab
This repository investigates the influence of different data augmentation strategies on MRI training performance.

Python · 8 stars
awesome-spine-mri
Awesome list about open-source spine MRI dataset.

6 stars
neuro.polymtl.ca
NeuroPoly's Website

Python · 4 stars
slicer-cart
Case Annotation and Review Tool (CART) Module for 3D Slicer

Python · 2 stars
neuropoly-db

Python · 1 star

Beginner friendly Everything

Open All

Add datasets from OpenNeuro Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

neuropoly/awesome-spine-mri#15 · Opened Sep 16, 2026
Weird text appearing on label when coming back to previous annotation Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

neuropoly/slicer-cart#216 · Opened Sep 11, 2026
Clarify output name Open

Difficulty 2/5 Under an hour Newbie friendliness 68/100

neuropoly/slicer-cart#215 · Opened Sep 11, 2026
Suggesting changing how names appear in the list Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

neuropoly/slicer-cart#214 · Opened Sep 11, 2026
Optimize Recursive BIDS Cohort Generator Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

neuropoly/slicer-cart#213 · Opened Sep 11, 2026
Add documentation on GH page Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

neuropoly/slicer-cart#212 · Opened Sep 8, 2026
Add editable version of logo Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

neuropoly/slicer-cart#211 · Opened Sep 8, 2026
Add spinal cord fmri dataset Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

neuropoly/awesome-spine-mri#14 · Opened Sep 8, 2026
[BugFixing Branch] Error when creating new columns on a blank cohort Open

[SUBJECT] Codebase [TASK] Core [TYPE] Error

Difficulty 3/5 1-2 days Newbie friendliness 65/100

neuropoly/slicer-cart#210 · 1 comment · Opened Sep 3, 2026
Support Slicer v5.12 Open

[SUBJECT] Codebase [TASK] Core [TYPE] Enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

neuropoly/slicer-cart#209 · Opened Sep 3, 2026
Beta Release Goals Open

[SUBJECT] Developer [TASK] Core [TYPE] Enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

neuropoly/slicer-cart#208 · Opened Sep 3, 2026
MR-RATE dataset Open

Difficulty 1/5 Under an hour Newbie friendliness 50/100

neuropoly/awesome-spine-mri#13 · Opened Aug 27, 2026
Problem with name of example displayed image Open

[SUBJECT] Codebase [TASK] Core [TYPE] Error Help Wanted

Difficulty 3/5 1-2 days Newbie friendliness 58/100

neuropoly/slicer-cart#206 · 1 comment · Opened Aug 21, 2026
install and running TotalSpineSeg-r20260730 Open

neuropoly/totalspineseg#147 · 4 comments · 1 assignee · Opened Aug 20, 2026
Bug with first line in list of cases Open

[SUBJECT] UX/UI [TASK] Core [TYPE] Error

Difficulty 3/5 1-2 days Newbie friendliness 42/100

neuropoly/slicer-cart#205 · 2 comments · Opened Aug 18, 2026
Add progress bar Open

[SUBJECT] UX/UI [TASK] Core [TYPE] Enhancement

Difficulty 3/5 1-2 days Newbie friendliness 65/100

neuropoly/slicer-cart#203 · 1 comment · Opened Aug 18, 2026
either with inheritance or simple tagging system define for each augmentation whether it is a GEO, TA, or GE. then the codebase can automatically based on this warn if the order of transforms is unusual, ... Open

neuropoly/SmaugLab#52 · 1 assignee · Opened Aug 7, 2026
crash if arguments do not exist for a transform (silently doing nothing) Open

neuropoly/SmaugLab#51 · 1 assignee · Opened Aug 7, 2026
easy validation that transform exists and config exists for it Open

neuropoly/SmaugLab#50 · 1 assignee · Opened Aug 7, 2026
easy sanity validation of a config before even running anything (undefined error crash, this is just silent behavior right now) Open

neuropoly/SmaugLab#49 · 1 assignee · Opened Aug 7, 2026
avoid name clash from transform vs. config name of that transform Open

neuropoly/SmaugLab#48 · 1 assignee · Opened Aug 7, 2026
Software setup: have one unified transform system Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

neuropoly/SmaugLab#44 · Opened Aug 3, 2026
Integrate `awesome-spine-mri` datasets in Neurobagel nodel Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

neuropoly/neuropoly-db#51 · Opened Jul 20, 2026
Integrate to `neurobagel` Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

neuropoly/awesome-spine-mri#12 · 1 comment · Opened Jul 20, 2026
Moving a cohort.csv to a new location breaks it on reopen Open

[SUBJECT] Codebase [TASK] Core [TYPE] Error

Difficulty 4/5 3-5 days Newbie friendliness 48/100

neuropoly/slicer-cart#201 · 3 comments · Opened Jul 17, 2026
Support one-resource-group-at-a-time review within a single case (multiple segmentations per subject) Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

neuropoly/slicer-cart#200 · Opened Jul 17, 2026
Add documentation about specifying keyboard shortcuts Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

neuropoly/slicer-cart#199 · 6 comments · Opened Jul 15, 2026
Removing column does not work Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

neuropoly/slicer-cart#198 · 2 comments · Opened Jul 13, 2026
Are trained weights for folds 1–4 of r20251124 available for download? We would like to use multi-fold ensembling for clinical measurement applications. Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

neuropoly/totalspineseg#144 · 1 comment · Opened Jul 9, 2026
qform/sform of input NIfTI file should be the same for the markup/segmentation Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

neuropoly/slicer-cart#190 · 5 comments · Opened Jun 19, 2026
Display how output label file name will look like Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

neuropoly/slicer-cart#185 · 2 comments · Opened Jun 19, 2026
Profile should be initialized before creating a job Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

neuropoly/slicer-cart#181 · 1 comment · Opened Jun 19, 2026
Change display to make it more compact Open

collaboration enhancement neurobagel

Difficulty 4/5 3-5 days Newbie friendliness 35/100

neuropoly/neuropoly-db#36 · Opened May 29, 2026
Cohort file edit not working for generic classification Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

neuropoly/slicer-cart#175 · 1 comment · Opened May 29, 2026
Add a button to fill volume Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

neuropoly/slicer-cart#172 · 1 comment · Opened May 29, 2026
Cohort file cannot be opened Open

[TYPE] Error

Difficulty 3/5 1-2 days Newbie friendliness 35/100

neuropoly/slicer-cart#166 · 10 comments · 1 reaction · Opened May 26, 2026
Broken links in segmentation task description Open

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

neuropoly/slicer-cart#158 · 1 comment · Opened May 11, 2026
Disc labeling failing in tSCI Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

neuropoly/totalspineseg#138 · 1 reaction · Opened May 7, 2026
BIDS metadata standard Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

neuropoly/neuropoly-db#26 · 1 comment · Opened May 6, 2026
Interoperabilty with other Slicer modules Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

neuropoly/slicer-cart#156 · Opened May 6, 2026
Feature Request: Empty Mask Save Confirmation Open

Difficulty 3/5 1-2 days Newbie friendliness 65/100

neuropoly/slicer-cart#155 · Opened May 6, 2026
SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1081) Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

neuropoly/neuropoly-db#21 · 1 comment · Opened Apr 30, 2026
`AccessLink` needed? Open

collaboration neurobagel

Difficulty 5/5 Over a week Newbie friendliness 25/100

neuropoly/neuropoly-db#20 · Opened Apr 30, 2026
Remove phenotypic row by default Open

collaboration neurobagel

Difficulty 3/5 1-2 days Newbie friendliness 35/100

neuropoly/neuropoly-db#19 · Opened Apr 30, 2026
Dragging a File/Folder into a `PathLineEdit` widget prevent further interactions with the GUI [MacOS] Open

[SUBJECT] Codebase [TASK] Core [TYPE] Error Help Wanted

Difficulty 3/5 1-2 days Newbie friendliness 52/100

neuropoly/slicer-cart#151 · 5 comments · Opened Apr 29, 2026
Data sharing instructions not up to date Open

Difficulty 1/5 Under an hour Newbie friendliness 68/100

neuropoly/intranet.neuro.polymtl.ca#167 · Opened Apr 27, 2026
[ENH] Neurobagel query result formatting (download) Open

neuropoly/neuropoly-db#10 · 6 assignees · Opened Apr 20, 2026
Cases with L6, or T13 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

neuropoly/totalspineseg#136 · 2 comments · Opened Apr 16, 2026
Identify the views with consistent colors Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

neuropoly/slicer-cart#150 · Opened Apr 3, 2026
Allow CART to stop once started Open

Difficulty 5/5 Over a week Newbie friendliness 38/100

neuropoly/slicer-cart#148 · 1 comment · Opened Apr 3, 2026

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