Open Nilser3 opened 11 months ago
Thank you for spotting this @Nilser3 🙏
In any case, I think that our plan was to re-create all SC segmentations using the contrast-agnostic model. So I would suggest to:
Does that make sense?
Hi @jcohenadad
Thanks to the help of @naga-karthik and @sandrinebedard
I have executed the contrast-agnostic model on the basel-mp2rage
and marseille-3T-mp2rage
datas
python monai/run_inference_single_image.py --path-img /mnt/nvme/nilaia/basel-mp2rage/sub-P121/anat/sub-P121_UNIT1.nii.gz --chkp-path /mnt/duke/temp/muena/contrast-agnostic/final_monai_model/nnunet_nf\=32_DS\=1_opt\=adam_lr\=0.001_AdapW_CCrop_bs\=2_64x192x320_20230918-2253/ --path-out test_contrast_agnostic --device cpu
sub-P121
:I have binarized the soft masks with a threshold of 0.5, and my issue persists in 137 patients out of 180 subjects.
I think we should retrain a new SC soft model with these soft masks in mp2rage datas.
I have binarized the soft masks with a threshold of 0.5, and my issue persists in 137 patients out of 180 subjects. I think we should retrain a new SC soft model with these soft masks in mp2rage datas.
Agreed. Could you please manually correct these 137 patients? Thanks! Good job!
To fix the MS lesion masks outside the SC, I first made a manual correction based on binarized contrast-agnostic SC masks. Then I made a union of these corrected SC masks with MS lesions (lesion-manualNeuroPoly.nii.gz) masks.
Here is the QC for basel-mp2rage
dataset from sub-P001
to sub-P086
Legend of QC maks
I suggest we put a hold on the correction of the masks until this issue is settled: https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/issues/99
Model available in : duke/temp/muena/contrast-agnostic/monai_bin_model
For basel-mp2rage
dataset (here the QC), I observe that the masks generated by this latest version are closer to those of the GT (manual correction based on version v2.0) for sub-P001
to sub-P086
.
Same observations on marseille-3T-mp2rage
dataset (here the QC), where even in the presence of large MS lesions, the latest model performs slightly better than the previous one.
Legend of QC:
@jcohenadad I still have to manually correct 203 subjects from basel-mp2rage
and all nih-ms-mp2rage
, maybe I should finish these correctiones based on the latest version instead of version 2.0 ?
@jcohenadad I still have to manually correct 203 subjects from basel-mp2rageand all nih-ms-mp2rage, maybe I should finish these correctiones based on the latest version instead of version 2.0 ?
what do you mean by "finish these corrections based on the latest version instead of version 2.0"? did you mean:
if you meant "1", then yes, I agree. Also, only do 20 subj and show me for validation before moving forward
I meant 1, run the latest version and then perform the manual correction. perfect, I will do so
Description
139 subjects of the 180 MS subjects in the
basel-mp2rage
database have lesion segmentation pixels (lesion-manualNeuroPoly mask) that are outside the SC segmentationHere an example:
sub-P121
sub-P001
,sub-P003
,sub-P004
,sub-P005
,sub-P006
,sub-P007
,sub-P010
,sub-P011
,sub-P012
,sub-P013
,sub-P014
,sub-P016
,sub-P019
,sub-P021
,sub-P022
,sub-P023
,sub-P024
,sub-P025
,sub-P026
,sub-P027
,sub-P028
,sub-P030
,sub-P031
,sub-P033
,sub-P034
,sub-P035
,sub-P036
,sub-P037
,sub-P038
,sub-P039
,sub-P040
,sub-P041
,sub-P042
,sub-P044
,sub-P045
,sub-P047
,sub-P050
,sub-P051
,sub-P053
,sub-P055
,sub-P056
,sub-P057
,sub-P058
,sub-P059
,sub-P061
,sub-P062
,sub-P063
,sub-P065
,sub-P066
,sub-P067
,sub-P068
,sub-P069
,sub-P070
,sub-P071
,sub-P072
,sub-P075
,sub-P078
,sub-P079
,sub-P082
,sub-P084
,sub-P085
,sub-P086
,sub-P087
,sub-P088
,sub-P094
,sub-P095
,sub-P096
,sub-P097
,sub-P098
,sub-P099
,sub-P100
,sub-P101
,sub-P103
,sub-P104
,sub-P106
,sub-P108
,sub-P109
,sub-P110
,sub-P111
,sub-P112
,sub-P114
,sub-P116
,sub-P117
,sub-P119
,sub-P120
,sub-P121
,sub-P122
,sub-P124
,sub-P125
,sub-P129
,sub-P130
,sub-P132
,sub-P134
,sub-P138
,sub-P139
,sub-P141
,sub-P142
,sub-P144
,sub-P145
,sub-P146
,sub-P148
,sub-P149
,sub-P151
,sub-P153
,sub-P156
,sub-P157
,sub-P160
,sub-P161
,sub-P165
,sub-P167
,sub-P169
,sub-P170
,sub-P173
,sub-P174
,sub-P175
,sub-P176
,sub-P178
,sub-P179
,sub-P180
,sub-P181
,sub-P182
,sub-P183
,sub-P185
,sub-P187
,sub-P188
,sub-P190
,sub-P191
,sub-P192
,sub-P194
,sub-P197
,sub-P199
,sub-P200
,sub-P241
,sub-P242
,sub-P243
,sub-P244
,sub-P246
,sub-P249
,sub-P250
Maybe we should redefine the SC masks by making a union of the MS lesions and current SC masks