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sct-pipeline
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contrast-agnostic-softseg-spinalcord
Contrast-agnostic spinal cord segmentation project with softseg
MIT License
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Clean up processing and repository
#64
sandrinebedard
closed
9 months ago
2
Disc labels files created by `process_data.sh` are empty for `sub-brnoUhb` and `sub-tokyo750w` sites
#63
valosekj
closed
9 months ago
2
Cleanup repos
#62
jcohenadad
closed
8 months ago
2
aggregated dataset: add monai-based scripts for conversion, training, and inference
#61
louisfb01
closed
8 months ago
1
add monai-based scripts for dataset conversion, training, and inference
#60
naga-karthik
closed
9 months ago
12
Memory issue with training on Monai with large datasets
#59
louisfb01
opened
1 year ago
19
Add script to compute CSA binarized and run QC on binarized prediction for ivadomed
#58
sandrinebedard
closed
11 months ago
0
Modify post processing nnunet for CSA computation and QC report
#57
sandrinebedard
closed
11 months ago
0
Work on a test notebook to identify the problem step by step and visualize each step of the pre-processing.
#56
louisfb01
closed
9 months ago
1
Try with much smaller patch sizes (based on nnunet recommended size @ebadrian ?).
#55
louisfb01
closed
9 months ago
1
Fix shape mismatch with different input sized UnetR training script
#54
louisfb01
closed
4 months ago
2
Add subjects with missing contrasts to exclude
#53
sandrinebedard
closed
1 year ago
0
UnetR training script
#52
louisfb01
closed
9 months ago
3
Training and evaluation scripts MICCAI 2023
#51
ebadrian
closed
1 year ago
0
Add processing of datasets with pathology
#50
sandrinebedard
closed
1 year ago
0
Update README on how to run training
#49
sandrinebedard
closed
9 months ago
1
Train on with other seeds
#48
sandrinebedard
opened
1 year ago
3
Verify whether softseg model performs well on images with spinal cord compression
#47
joshuacwnewton
closed
2 months ago
6
Fix MTS filenames in preprocessing and charts scripts
#46
sandrinebedard
closed
1 year ago
0
Optimize DA
#45
jcohenadad
closed
9 months ago
2
Fix filenames for MTS in processing script
#44
sandrinebedard
closed
1 year ago
0
Add command for CSA charts
#43
sandrinebedard
closed
1 year ago
0
Change file names for MTS contrasts
#42
sandrinebedard
closed
1 year ago
0
Revise CenterCrop
#41
jcohenadad
closed
9 months ago
3
For final model, do hyperparam optimization
#40
jcohenadad
closed
9 months ago
3
For final model, use 0.8/0.2 train/validation
#39
jcohenadad
opened
1 year ago
0
Filtering not effective
#38
jcohenadad
closed
11 months ago
1
freeze version for OHBM
#37
jcohenadad
closed
9 months ago
1
Cleanup branches
#36
jcohenadad
closed
11 months ago
1
use _pred, not _pred_painted & remove 4th dimension
#35
sandrinebedard
closed
1 year ago
0
_pred has 4 dimensions, not able to compute CSA
#34
sandrinebedard
closed
1 year ago
0
Remove extreme slices in the T2w space to avoid partial segmentations
#33
jcohenadad
closed
1 year ago
1
Changed intercontrast registration algo
#32
jcohenadad
closed
1 year ago
0
Compute CSA on prediction mask
#31
sandrinebedard
closed
1 year ago
0
CSA charts preliminary notebook
#30
ebadrian
closed
1 year ago
0
Add b=0 scan from the DWI sequence as a new contrast for training model
#29
jcohenadad
opened
1 year ago
3
Joblib generator for subject consistency across different contrast trainings
#28
uzaymacar
closed
11 months ago
1
Analyse CSA
#27
sandrinebedard
closed
8 months ago
2
Modify preprocessing script
#26
sandrinebedard
closed
1 year ago
1
Training separately on the two `MTS` contrasts
#25
uzaymacar
closed
9 months ago
6
`NaN` in T2w softseg labels
#24
uzaymacar
opened
1 year ago
1
Compute CSA on GT and output prediction mask
#23
sandrinebedard
closed
9 months ago
5
Merge processing pipelines
#22
sandrinebedard
closed
2 years ago
0
Configs for cropped training
#21
uzaymacar
closed
11 months ago
1
Preprocessing for extracting the spinal cord ROI via centerline estimation.
#20
uzaymacar
closed
11 months ago
2
Removed .idea folder
#19
uzaymacar
closed
2 years ago
0
Configs for contrast-specific models
#18
uzaymacar
closed
2 years ago
1
Configs for super-duper single and per-contrast models
#17
uzaymacar
closed
2 years ago
2
Consistency regularization
#16
jcohenadad
opened
2 years ago
0
Update analysis script to be standalone for reproducing the training dataset
#15
jcohenadad
opened
2 years ago
1
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