ivadomed utilities issues

ivadomed / 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