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ivadomed
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utilities
Repository containing utility scripts for handling various aspects in a DL model training pipeline
MIT License
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Remove `MetricsReloaded` scripts
#53
valosekj
closed
3 months ago
0
Consider moving `compute_metrics/compute_metrics_reloaded.py` to `ivadomed/MetricsReloaded`
#52
valosekj
closed
3 months ago
2
`compute_metrics_reloaded.py` - consider other output type than CSV
#51
valosekj
opened
3 months ago
1
Add lesion-wise metrics
#50
valosekj
closed
3 months ago
2
Add lesion-wise metrics to `compute_metrics_reloaded.py`
#49
valosekj
closed
3 months ago
1
Small improvements of metrics reloaded script
#48
valosekj
closed
3 months ago
1
Create documentation and script to use SPINEPS for discs labeling
#47
NathanMolinier
closed
2 months ago
2
Add python script and quick start guide for MetricsReloaded
#46
valosekj
closed
4 months ago
8
Document the errors during nnUnet installation on `rosenberg`
#45
jcohenadad
closed
6 months ago
5
`convert_bids_to_nnUNetV2.py` - add support of data types other than `anat`
#44
rohanbanerjee
closed
6 months ago
2
The `convert_bids_to_nnUNetV2.py` script is not compatible with datatypes other than `anat`
#43
rohanbanerjee
closed
6 months ago
3
`Dice Loss` vs `Dice Loss with smooting term`
#42
valosekj
opened
6 months ago
12
Plot nnUNet training log
#41
valosekj
closed
7 months ago
2
Add new scripts to analyze BIDS compliant datasets
#40
NathanMolinier
opened
9 months ago
1
Fix nnUNetPredictor inference
#39
hermancollin
closed
10 months ago
1
nnUNetPredictor available in newest nnUNetv2 pip package
#38
hermancollin
closed
10 months ago
5
Inference script: postprocess range from [0,1] to [0,255]
#37
hermancollin
closed
11 months ago
2
How to avoid inference script duplication
#36
hermancollin
opened
11 months ago
1
Script to visualize preprocessed images as per nnUNet `plans.json`
#35
rohanbanerjee
opened
11 months ago
1
Add `run_inference_single_subject.py` script
#34
valosekj
closed
11 months ago
1
Inference fails with --path-images and multiple images
#33
hermancollin
closed
10 months ago
3
How are model checkpoints packaged?
#32
hermancollin
opened
11 months ago
3
Add `run_inference_single_subject.py` script
#31
valosekj
closed
11 months ago
0
Dataset use: How to be efficient with BIDS datasets
#30
NathanMolinier
opened
11 months ago
1
New lighter SCT image class
#29
NathanMolinier
closed
11 months ago
5
Convert softseg values to integer values
#28
tzebre
opened
1 year ago
0
corrective on line 228
#27
tzebre
closed
1 year ago
0
Add script to extract images from Bids dataset to a folder
#26
tzebre
closed
1 year ago
0
Add a script to merge 2 nnUNet dataset
#25
tzebre
closed
1 year ago
0
Write a script for running MONAI inference
#24
valosekj
opened
1 year ago
0
Post-processing not included in run_inference.py
#23
plbenveniste
opened
1 year ago
3
Document in README presence of script to run inference in NIfTI image
#22
jcohenadad
closed
1 year ago
1
Script to take BIDS dataset and generate MONAI-compatible JSON list of subjects for training
#21
jcohenadad
opened
1 year ago
4
json creation when converting from nnUNetV2 to BIDS
#20
tzebre
opened
1 year ago
8
Note sections are not rendered properly
#19
valosekj
closed
1 year ago
1
Move nnU-Net quick-start guide from `ivadomed/training-nnunet` repo
#18
valosekj
closed
1 year ago
0
Add softseg support for BIDS to nnUNetv2 conversion script
#17
valosekj
closed
1 year ago
0
Add softseg support for nnUNet
#16
valosekj
opened
1 year ago
3
Create a script to convert from nnUNet V2 to BIDS
#15
tzebre
closed
1 year ago
4
Potential bug in the dataset split in the conversion script
#14
rohanbanerjee
closed
1 year ago
2
Update nnUNet conversion script to v2
#13
valosekj
closed
1 year ago
7
BIDS to nnUNet V2 new version based on Jan pull request #11
#12
tzebre
closed
1 year ago
1
Update BIDS to nnUnet conversion script to nnUnet v2
#11
valosekj
closed
1 year ago
1
BIDS subject number lost in conversion to nnUNet dataset format
#10
rohanbanerjee
closed
1 year ago
2
Rename repository to "utilities" instead of "templates"?
#9
naga-karthik
closed
1 year ago
5
Create dataset splits for training with nnUNet
#8
naga-karthik
closed
1 year ago
0
Check whether image and label files exist before adding them to JSON file
#7
naga-karthik
closed
1 year ago
1
`create_msd_json_from_bids.py` - missing `ses-` tag for labels
#6
valosekj
closed
1 year ago
2
Template for 2d microscopy segmentation
#5
hermancollin
closed
1 year ago
1
For script flags, replace "_" by "-"
#4
jcohenadad
closed
1 year ago
1
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