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sct-pipeline
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ukbiobank-spinalcord-csa
Measure of the averaged cross-sectional area (cord CSA) between C2 and C3 of the spinal cord with UK Biobank Brain MRI dataset.
MIT License
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How to get coeff.grad file
#86
karllandheer
closed
10 months ago
3
Add statistics for PMJ-based CSA and compute distance from C2-C3 and PMJ
#85
sandrinebedard
closed
3 years ago
2
Add scatterplot of PMJ-based CSA vs C2-C3-based CSA in `compute_stats.py`
#84
sandrinebedard
closed
3 years ago
0
Compute distance between PMJ and C2-C3 disc
#83
sandrinebedard
closed
3 years ago
0
Add manual labeling of PMJ in `manual_correction.py`
#82
sandrinebedard
closed
3 years ago
0
Add pmj labeling and CSA from PMJ in processing pipeline
#81
sandrinebedard
closed
3 years ago
0
Add manual labeling of PMJ label in `manual_correction.py`
#80
sandrinebedard
closed
3 years ago
0
Apply normalization method and exclude subjects with neuro diseases in statistical analysis
#79
sandrinebedard
closed
3 years ago
2
Add PMJ detection in processing pipeline
#78
sandrinebedard
closed
3 years ago
0
Apply normalization of CSA in `compute_stats.py`
#77
sandrinebedard
closed
3 years ago
0
Exclude subjects with history of neurological, cognitive or psychological diseases
#76
sandrinebedard
closed
3 years ago
0
Add images with motion artifacts to exclude.yml
#75
sandrinebedard
closed
3 years ago
1
Adjust statistical analysis for the updated pipeline and exploration
#74
sandrinebedard
closed
3 years ago
3
Consider moving `exclude.yml` to `git@data.neuro.polymtl.ca:datasets/uk-biobank-processed`
#73
sandrinebedard
opened
3 years ago
0
Add subjects with wrong FOV to exclude.yml
#72
sandrinebedard
closed
3 years ago
0
Create release of this repository and add release tag info in README of dataset
#71
jcohenadad
closed
3 years ago
2
Start tagging releases of dataset so we can include that information in the derivatives
#70
jcohenadad
opened
3 years ago
0
Adapt for new yml format in package_for_correction.py
#69
sandrinebedard
closed
3 years ago
0
Add subjects with wrong FOV to exclude.yml
#68
sandrinebedard
closed
3 years ago
0
Workflow for manual labeling
#67
sandrinebedard
opened
3 years ago
0
Change yml scheme to adapt for new list format
#66
sandrinebedard
closed
3 years ago
0
Add subjects to exclude
#65
sandrinebedard
closed
3 years ago
0
Remove ANTS in dependencies
#64
sandrinebedard
opened
3 years ago
0
Update installation instructions for `gradunwarp` and SCT v5.3.0
#63
joshuacwnewton
closed
3 years ago
1
Change YAML scheme for uk_manual_correction
#62
sandrinebedard
closed
3 years ago
0
Poor data quality: T1w
#61
sandrinebedard
opened
3 years ago
0
Add subjects to exclude
#60
sandrinebedard
closed
3 years ago
4
display warp: fullWarp_abs.nii.gz is invalid: should be encoded in a 5D file with vector intent code
#59
sandrinebedard
opened
3 years ago
4
Update sct version in dependencies
#58
sandrinebedard
closed
3 years ago
0
Add tutorial for manual vertebral labeling
#57
sandrinebedard
closed
3 years ago
0
Add subjects to exclude from next 650 subjects
#56
sandrinebedard
closed
3 years ago
1
Add manually qc-ed automatic segmentations to derivatives
#55
sandrinebedard
closed
3 years ago
0
Add sub-1024305_T1w.nii.gz to exclude.yml
#54
sandrinebedard
closed
3 years ago
0
add 2 images to exclude.yml
#53
sandrinebedard
closed
3 years ago
0
Remove T2w processing in process_data.sh
#52
sandrinebedard
closed
3 years ago
0
Create derivative and json sidecar for QC-ed automatic segmentations
#51
sandrinebedard
closed
3 years ago
3
Remove T2w processing in processing pipeline
#50
sandrinebedard
closed
3 years ago
0
add subjects to exclude from sub-1000032 to sub-1025290
#49
sandrinebedard
closed
3 years ago
4
add sub to exclude from QC: sub-1025351 to sub-1047836
#48
sandrinebedard
closed
3 years ago
0
Bypass registration to PAM50 template in process_data.sh
#47
sandrinebedard
closed
3 years ago
0
Add script package_for_correction.py as cli
#46
sandrinebedard
closed
3 years ago
0
Poor data quality : T2w FLAIR
#45
sandrinebedard
opened
3 years ago
0
Suggestion to bypass registration to PAM50 template
#44
jcohenadad
closed
3 years ago
0
Workflow for manual correction
#43
jcohenadad
opened
3 years ago
0
Compute mean dice coeff of segmentations from candidates
#42
sandrinebedard
closed
3 years ago
1
Add exclude.yml list
#41
sandrinebedard
closed
3 years ago
1
Add script to compare .yml files for test 1 of manual seg
#40
sandrinebedard
closed
3 years ago
1
Check if ITK-SNAP exists, exits program if not in manual_correction.py
#39
sandrinebedard
closed
3 years ago
10
Check if command "ITK-SNAP" for windows exists in manual_correction.py
#38
sandrinebedard
closed
3 years ago
0
Add a file that lists subjects to exclude
#37
jcohenadad
closed
3 years ago
1
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