sct-pipeline ukbiobank-spinalcord-csa issues

sct-pipeline / 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