sct-pipeline contrast-agnostic-softseg-spinalcord issues

sct-pipeline / contrast-agnostic-softseg-spinalcord

Contrast-agnostic spinal cord segmentation project with softseg

MIT License

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Re-run preprocessing to include combinations of contrasts

#112 sandrinebedard opened 5 days ago
0
Training SynthSeg on spine-generic data

#111 naga-karthik opened 2 weeks ago
6
Consider moving this repository to ivadomed

#110 jcohenadad opened 3 weeks ago
0
Inconsistent list of subject used for training

#109 jcohenadad closed 3 weeks ago
7
Testing contrast-agnostic model on GRE magnitude data

#108 jcohenadad opened 1 month ago
1
QC compression results between monai and deepseg_2d models

#107 naga-karthik opened 1 month ago
1
run_inference_single_image.py v1 vs v2

#106 jcohenadad closed 3 weeks ago
3
Update preprocessing script for spine-generic with new naming convention

#105 sandrinebedard closed 3 months ago
1
Continual training of `contrast-agnostic` model with new contrasts and pathologies

#104 naga-karthik closed 3 weeks ago
0
Add reorientation to RPI also for train/val transforms

#103 valosekj closed 2 months ago
3
Naming convention for adding new contrasts to the training set

#102 naga-karthik opened 4 months ago
12
Create scripts to reproduce results

#101 jcohenadad opened 5 months ago
1
Simplify inference script

#100 naga-karthik closed 5 months ago
0
Consider binarizing the ground truth after averaging across contrasts, before training a softseg model

#99 jcohenadad opened 5 months ago
3
What threshold to use on model prediction?

#98 jcohenadad closed 4 months ago
2
add info about dataset split used for training contrast-agnostic model

#97 naga-karthik closed 5 months ago
0
Add mirroring test-time augmentation

#96 naga-karthik opened 6 months ago
2
Make inference CLI callable from anywhere

#95 jcohenadad closed 6 months ago
0
Make CLI callable from anywhere

#94 jcohenadad closed 6 months ago
0
Fixed documentation on inference (follow-up)

#93 jcohenadad closed 6 months ago
0
Doc points to non-existing file

#92 jcohenadad closed 6 months ago
1
Fixed documentation on inference

#91 jcohenadad closed 6 months ago
1
Port towards config file-based training

#90 naga-karthik closed 4 months ago
0
Extend model to also segment the CSF

#89 jcohenadad opened 7 months ago
0
Update readme with citation info and arxiv badge

#88 naga-karthik closed 7 months ago
0
Implement strategy for assessing the quality of the model during lifelong training

#87 jcohenadad opened 8 months ago
2
Slow repo cloning

#86 valosekj closed 8 months ago
6
Adding feature to load weights from pre-trained checkpoint

#85 rohanbanerjee opened 8 months ago
0
Strategy to re-use existing binary ground truth for enriching contrast-agnostic model

#84 jcohenadad closed 4 months ago
26
Re-train `contrast-agnostic` model with `EPI` data

#83 rohanbanerjee opened 8 months ago
1
Add anova test on soft all and hard all

#82 sandrinebedard closed 8 months ago
0
add anima metrics

#81 naga-karthik closed 8 months ago
1
Finalise script for figures

#80 sandrinebedard closed 8 months ago
0
Upgrade and pin monai to 1.3.0

#79 naga-karthik closed 8 months ago
0
Update main readme

#78 naga-karthik closed 8 months ago
0
add qc generation script for epi data

#77 naga-karthik closed 8 months ago
0
add requirements for gpu inference

#76 naga-karthik closed 8 months ago
1
Running into errors while using `--device gpu` while running inference using MONAI

#75 rohanbanerjee closed 8 months ago
3
Test contrast-agnostic model in Marseille 7T T2S data

#74 Nilser3 opened 9 months ago
0
Add post-processing code to further improve prediction

#73 jcohenadad closed 3 weeks ago
1
Errors while using the `monai` training script for the EPI data

#72 rohanbanerjee closed 9 months ago
4
Prediction clipping sets background values to 0.5 instead of 0

#71 valosekj closed 9 months ago
2
When to center crop images at test-time

#70 naga-karthik opened 9 months ago
1
Augmentation with intensity scaling

#69 naga-karthik opened 9 months ago
0
Analysis for the paper

#68 sandrinebedard closed 9 months ago
3
Compute CSA prediction error

#67 sandrinebedard closed 9 months ago
5
One outlier subject in the softseg CSA of T1w contrast

#66 naga-karthik closed 9 months ago
7
Naga/nnunet

#65 sandrinebedard closed 11 months ago
0
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