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ivadomed / model_seg_ms_mp2rage

Model repository for MS lesion segmentation on MP2RAGE data from University of Basel
MIT License
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MS lesions masks outside the SC mask #79

Closed Nilser3 closed 12 months ago

Nilser3 commented 12 months ago

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 segmentation

Here an example:

sub-P121

lesion_SC List of subjects with this issue: 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

jcohenadad commented 12 months ago

@Nilser3 this issue refers to the data, not to the model-- can you please move this issue to https://github.com/neuropoly/data-management/issues and I will then comment there-- thanks!

Nilser3 commented 12 months ago

This issue is closed, and a new one is opened in the correct repo (the issue could not be transferred because they are different organizations ivadomed/model_seg_ms_mp2rage and neuropoly/data-managemment )