QC of datasets

[plbenveniste]

I ran QC on every dataset to check if lesions were segmented outside the spinal cord.
The QC was ran with dataset_aggregation/qc_datasets.py. It is stored in duke/temp/plben/ms-lesion-agnostic/qc_datasets.
It segments the spinal cord and displays the QC of the lesion segmentation on the image cropped around the spinal cord (dilated by 4 voxels).
Further, if lesions are outside the spinal cord, the file name are stored in a .txt file at the end of the script.

[plbenveniste]

Here are the files which were detected as having lesions outside of the spinal cord. The QC output are stored in

File list

Lesions outside the SC:
basel-mp2rage/derivatives/labels/sub-P241/anat/sub-P241_UNIT1_desc-rater3_label-lesion_seg.nii.gz
basel-mp2rage/derivatives/labels/sub-P167/anat/sub-P167_UNIT1_desc-rater3_label-lesion_seg.nii.gz
basel-mp2rage/derivatives/labels/sub-P027/anat/sub-P027_UNIT1_desc-rater3_label-lesion_seg.nii.gz
basel-mp2rage/derivatives/labels/sub-P065/anat/sub-P065_UNIT1_desc-rater3_label-lesion_seg.nii.gz
basel-mp2rage/derivatives/labels/sub-P130/anat/sub-P130_UNIT1_desc-rater3_label-lesion_seg.nii.gz
basel-mp2rage/derivatives/labels/sub-P024/anat/sub-P024_UNIT1_desc-rater3_label-lesion_seg.nii.gz
basel-mp2rage/derivatives/labels/sub-P085/anat/sub-P085_UNIT1_desc-rater3_label-lesion_seg.nii.gz
basel-mp2rage/derivatives/labels/sub-P153/anat/sub-P153_UNIT1_desc-rater3_label-lesion_seg.nii.gz
basel-mp2rage/derivatives/labels/sub-P075/anat/sub-P075_UNIT1_desc-rater3_label-lesion_seg.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m281109/ses-20190403/anat/sub-m281109_ses-20190403_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m717393/ses-20210423/anat/sub-m717393_ses-20210423_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m717393/ses-20210423/anat/sub-m717393_ses-20210423_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m058483/ses-20211126/anat/sub-m058483_ses-20211126_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m843491/ses-20150517/anat/sub-m843491_ses-20150517_acq-ax_chunk-3_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m843491/ses-20200814/anat/sub-m843491_ses-20200814_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m168132/ses-20150414/anat/sub-m168132_ses-20150414_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m381960/ses-20180120/anat/sub-m381960_ses-20180120_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m693874/ses-20211216/anat/sub-m693874_ses-20211216_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m594395/ses-20180112/anat/sub-m594395_ses-20180112_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m243881/ses-20081112/anat/sub-m243881_ses-20081112_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m043238/ses-20190916/anat/sub-m043238_ses-20190916_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m312155/ses-20140103/anat/sub-m312155_ses-20140103_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m312155/ses-20140103/anat/sub-m312155_ses-20140103_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m023917/ses-20130506/anat/sub-m023917_ses-20130506_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m982446/ses-20151104/anat/sub-m982446_ses-20151104_acq-ax_chunk-3_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m982446/ses-20151104/anat/sub-m982446_ses-20151104_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m747680/ses-20171110/anat/sub-m747680_ses-20171110_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m549151/ses-20210126/anat/sub-m549151_ses-20210126_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m519216/ses-20171221/anat/sub-m519216_ses-20171221_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m519216/ses-20180829/anat/sub-m519216_ses-20180829_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m519216/ses-20180829/anat/sub-m519216_ses-20180829_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m778290/ses-20151217/anat/sub-m778290_ses-20151217_acq-ax_chunk-3_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m362157/ses-20190913/anat/sub-m362157_ses-20190913_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m358902/ses-20110406/anat/sub-m358902_ses-20110406_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m701054/ses-20141201/anat/sub-m701054_ses-20141201_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m425924/ses-20180712/anat/sub-m425924_ses-20180712_acq-ax_chunk-4_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m002126/ses-20100716/anat/sub-m002126_ses-20100716_acq-ax_chunk-1_T2w_lesion-manual.nii.gz
bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m002126/ses-20100716/anat/sub-m002126_ses-20100716_acq-ax_chunk-2_T2w_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon198/ses-M0/anat/sub-mon198_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon034/ses-M0/anat/sub-mon034_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon211/ses-M0/anat/sub-mon211_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-tor010/ses-M0/anat/sub-tor010_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon118/ses-M0/anat/sub-mon118_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal158/ses-M0/anat/sub-cal158_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon050/ses-M0/anat/sub-mon050_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal152/ses-M0/anat/sub-cal152_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-edm019/ses-M0/anat/sub-edm019_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-tor128/ses-M0/anat/sub-tor128_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon168/ses-M0/anat/sub-mon168_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal167/ses-M0/anat/sub-cal167_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-edm107/ses-M0/anat/sub-edm107_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon092/ses-M0/anat/sub-mon092_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-edm038/ses-M0/anat/sub-edm038_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon191/ses-M0/anat/sub-mon191_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal114/ses-M0/anat/sub-cal114_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal156/ses-M0/anat/sub-cal156_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-edm173/ses-M0/anat/sub-edm173_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-tor035/ses-M0/anat/sub-tor035_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-tor070/ses-M0/anat/sub-tor070_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal094/ses-M0/anat/sub-cal094_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon148/ses-M0/anat/sub-mon148_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal130/ses-M0/anat/sub-cal130_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-van111/ses-M0/anat/sub-van111_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal154/ses-M0/anat/sub-cal154_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon113/ses-M0/anat/sub-mon113_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon119/ses-M0/anat/sub-mon119_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-van206/ses-M0/anat/sub-van206_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon193/ses-M0/anat/sub-mon193_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon138/ses-M0/anat/sub-mon138_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-tor049/ses-M0/anat/sub-tor049_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon141/ses-M0/anat/sub-mon141_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal192/ses-M0/anat/sub-cal192_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-edm161/ses-M0/anat/sub-edm161_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon160/ses-M0/anat/sub-mon160_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-tor012/ses-M12/anat/sub-tor012_ses-M12_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-mon079/ses-M0/anat/sub-mon079_ses-M0_PSIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-cal149/ses-M0/anat/sub-cal149_ses-M0_STIR_lesion-manual.nii.gz
canproco/derivatives/labels/sub-edm078/ses-M0/anat/sub-edm078_ses-M0_PSIR_lesion-manual.nii.gz
ms-basel-2018/derivatives/labels/sub-5505/ses-20180903/anat/sub-5505_ses-20180903_acq-sagTse_T2w_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-013/ses-20170607/anat/sub-013_ses-20170607_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-013/ses-20170607/anat/sub-013_ses-20170607_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-007/ses-20170103/anat/sub-007_ses-20170103_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-014/ses-20200116/anat/sub-014_ses-20200116_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-010/ses-20180918/anat/sub-010_ses-20180918_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-010/ses-20180918/anat/sub-010_ses-20180918_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-003/ses-20190302/anat/sub-003_ses-20190302_acq-sagThorTSE_run-1_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-009/ses-20180627/anat/sub-009_ses-20180627_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-004/ses-20170209/anat/sub-004_ses-20170209_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-004/ses-20170209/anat/sub-004_ses-20170209_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-015/ses-20200128/anat/sub-015_ses-20200128_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-015/ses-20200128/anat/sub-015_ses-20200128_acq-sagThorTSE_run-1_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-006/ses-20180814/anat/sub-006_ses-20180814_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-001/ses-20170622/anat/sub-001_ses-20170622_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-012/ses-20170710/anat/sub-012_ses-20170710_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-012/ses-20170710/anat/sub-012_ses-20170710_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-016/ses-20180117/anat/sub-016_ses-20180117_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-016/ses-20180117/anat/sub-016_ses-20180117_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-005/ses-20180417/anat/sub-005_ses-20180417_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-005/ses-20180417/anat/sub-005_ses-20180417_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-008/ses-20180222/anat/sub-008_ses-20180222_acq-sagThorTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-008/ses-20180222/anat/sub-008_ses-20180222_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-002/ses-20190325/anat/sub-002_ses-20190325_acq-sagThorTSE_run-2_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-002/ses-20190325/anat/sub-002_ses-20190325_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-basel-2020/derivatives/labels/sub-011/ses-20170131/anat/sub-011_ses-20170131_acq-sagCervTSE_PD_lesion-manual.nii.gz
ms-karolinska-2020/derivatives/labels/sub-2038/ses-M0/anat/sub-2038_ses-M0_acq-ax_echo-1_MEGRE_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-119/anat/sub-119_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-138/anat/sub-138_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-148/anat/sub-148_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-114/anat/sub-114_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-155/anat/sub-155_acq-sag_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-122/anat/sub-122_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-036/anat/sub-036_acq-sag_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-146/anat/sub-146_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-139/anat/sub-139_acq-sag_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-120/anat/sub-120_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-120/anat/sub-120_acq-axInf_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-112/anat/sub-112_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-161/anat/sub-161_acq-sagSup_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-137/anat/sub-137_acq-sag_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-130/anat/sub-130_acq-sag_T2w_lesion-manual.nii.gz
ms-nyu/derivatives/labels/sub-123/anat/sub-123_acq-sagSup_T2w_lesion-manual.nii.gz
nih-ms-mp2rage/derivatives/labels/sub-nih069/anat/sub-nih069_UNIT1_desc-rater1_label-lesion_seg.nii.gz
nih-ms-mp2rage/derivatives/labels/sub-nih138/anat/sub-nih138_UNIT1_desc-rater1_label-lesion_seg.nii.gz
nih-ms-mp2rage/derivatives/labels/sub-nih169/anat/sub-nih169_UNIT1_desc-rater1_label-lesion_seg.nii.gz
nih-ms-mp2rage/derivatives/labels/sub-nih081/anat/sub-nih081_UNIT1_desc-rater1_label-lesion_seg.nii.gz
nih-ms-mp2rage/derivatives/labels/sub-nih150/anat/sub-nih150_UNIT1_desc-rater1_label-lesion_seg.nii.gz
sct-testing-large/derivatives/labels/sub-bwh055/anat/sub-bwh055_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi111/anat/sub-milanFilippi111_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd139/anat/sub-nyuShepherd139_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-lyonOfsep004/anat/sub-lyonOfsep004_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd112/anat/sub-nyuShepherd112_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich013/anat/sub-nihReich013_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi040/anat/sub-milanFilippi040_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich014/anat/sub-nihReich014_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi105/anat/sub-milanFilippi105_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-karoTobiasMS003/ses-01/anat/sub-karoTobiasMS003_ses-01_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd115/anat/sub-nyuShepherd115_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich026/anat/sub-nihReich026_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-bwh017/anat/sub-bwh017_acq-sagstir_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-vanderbiltSeth012/anat/sub-vanderbiltSeth012_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-bwh025/anat/sub-bwh025_acq-ax_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-bwh025/anat/sub-bwh025_acq-sagstir_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-vanderbiltSeth020/anat/sub-vanderbiltSeth020_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi112/anat/sub-milanFilippi112_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi068/anat/sub-milanFilippi068_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-bwh056/anat/sub-bwh056_acq-sagstir_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-karoTobiasMS014/ses-01/anat/sub-karoTobiasMS014_ses-01_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd130/anat/sub-nyuShepherd130_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich022/anat/sub-nihReich022_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi034/anat/sub-milanFilippi034_acq-ax_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd154/anat/sub-nyuShepherd154_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd123/anat/sub-nyuShepherd123_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-montpellierLesion006/anat/sub-montpellierLesion006_acq-inf_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich017/anat/sub-nihReich017_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd116/anat/sub-nyuShepherd116_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi076/anat/sub-milanFilippi076_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-karoTobiasMS021/ses-01/anat/sub-karoTobiasMS021_ses-01_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd105/anat/sub-nyuShepherd105_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-bwh061/anat/sub-bwh061_acq-ax_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-montpellierLesion010/anat/sub-montpellierLesion010_acq-sagcerv_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd148/anat/sub-nyuShepherd148_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd107/anat/sub-nyuShepherd107_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-amuVirginie020/anat/sub-amuVirginie020_acq-sup_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-karoTobiasMS030/ses-01/anat/sub-karoTobiasMS030_ses-01_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-lyonOfsep082/anat/sub-lyonOfsep082_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich020/anat/sub-nihReich020_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd113/anat/sub-nyuShepherd113_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd113/anat/sub-nyuShepherd113_acq-inf_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-ucsfTalbott010/anat/sub-ucsfTalbott010_acq-ax_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich033/anat/sub-nihReich033_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd132/anat/sub-nyuShepherd132_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd035/anat/sub-nyuShepherd035_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi058/anat/sub-milanFilippi058_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi058/anat/sub-milanFilippi058_acq-ax_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi025/anat/sub-milanFilippi025_acq-ax_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-bwh011/anat/sub-bwh011_acq-sagstir_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich005/anat/sub-nihReich005_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd141/anat/sub-nyuShepherd141_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-vanderbiltSeth003/anat/sub-vanderbiltSeth003_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich016/anat/sub-nihReich016_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-karoTobiasMS033/ses-01/anat/sub-karoTobiasMS033_ses-01_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-karoTobiasMS001/ses-01/anat/sub-karoTobiasMS001_ses-01_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi099/anat/sub-milanFilippi099_acq-ax_T2star_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi007/anat/sub-milanFilippi007_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nihReich011/anat/sub-nihReich011_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-milanFilippi087/anat/sub-milanFilippi087_acq-sag_T2w_lesion-manual.nii.gz
sct-testing-large/derivatives/labels/sub-nyuShepherd131/anat/sub-nyuShepherd131_acq-sag_T2w_lesion-manual.nii.gz

I will now QC each image to check what the problems seems to be.

[plbenveniste]

Review of files:
This review was extremely useful, I found lesions in the brain and brain stem in multiple dataset. Moreoever, I found some mistakes of segmentations corresponding to nothing in various locations of the images (peut être des ratures).

Tagging @naga-karthik, @Nilser3 and @jcohenadad.

File list

Lesions outside the SC:
- basel-mp2rage/derivatives/labels/sub-P241/anat/sub-P241_UNIT1_desc-rater3_label-lesion_seg.nii.gz # Brain stem
- basel-mp2rage/derivatives/labels/sub-P167/anat/sub-P167_UNIT1_desc-rater3_label-lesion_seg.nii.gz # The segmentation file is the same as the image file 
- basel-mp2rage/derivatives/labels/sub-P027/anat/sub-P027_UNIT1_desc-rater3_label-lesion_seg.nii.gz # Brain stem
- basel-mp2rage/derivatives/labels/sub-P065/anat/sub-P065_UNIT1_desc-rater3_label-lesion_seg.nii.gz # Brain stem
- basel-mp2rage/derivatives/labels/sub-P130/anat/sub-P130_UNIT1_desc-rater3_label-lesion_seg.nii.gz # Brain stem
- basel-mp2rage/derivatives/labels/sub-P024/anat/sub-P024_UNIT1_desc-rater3_label-lesion_seg.nii.gz # Brain stem
- basel-mp2rage/derivatives/labels/sub-P085/anat/sub-P085_UNIT1_desc-rater3_label-lesion_seg.nii.gz # Brain stem
- basel-mp2rage/derivatives/labels/sub-P153/anat/sub-P153_UNIT1_desc-rater3_label-lesion_seg.nii.gz # Brain stem
- basel-mp2rage/derivatives/labels/sub-P075/anat/sub-P075_UNIT1_desc-rater3_label-lesion_seg.nii.gz # Brain stem
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m281109/ses-20190403/anat/sub-m281109_ses-20190403_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m717393/ses-20210423/anat/sub-m717393_ses-20210423_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Brain stem
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m717393/ses-20210423/anat/sub-m717393_ses-20210423_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m058483/ses-20211126/anat/sub-m058483_ses-20211126_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m843491/ses-20150517/anat/sub-m843491_ses-20150517_acq-ax_chunk-3_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m843491/ses-20200814/anat/sub-m843491_ses-20200814_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m168132/ses-20150414/anat/sub-m168132_ses-20150414_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Problematic segmentation: lesion outside the body
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m381960/ses-20180120/anat/sub-m381960_ses-20180120_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m693874/ses-20211216/anat/sub-m693874_ses-20211216_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m594395/ses-20180112/anat/sub-m594395_ses-20180112_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m243881/ses-20081112/anat/sub-m243881_ses-20081112_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m043238/ses-20190916/anat/sub-m043238_ses-20190916_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m312155/ses-20140103/anat/sub-m312155_ses-20140103_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m312155/ses-20140103/anat/sub-m312155_ses-20140103_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m023917/ses-20130506/anat/sub-m023917_ses-20130506_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Lesion outside of the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m982446/ses-20151104/anat/sub-m982446_ses-20151104_acq-ax_chunk-3_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m982446/ses-20151104/anat/sub-m982446_ses-20151104_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m747680/ses-20171110/anat/sub-m747680_ses-20171110_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Lesion outside of the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m549151/ses-20210126/anat/sub-m549151_ses-20210126_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m519216/ses-20171221/anat/sub-m519216_ses-20171221_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m519216/ses-20180829/anat/sub-m519216_ses-20180829_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m519216/ses-20180829/anat/sub-m519216_ses-20180829_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m778290/ses-20151217/anat/sub-m778290_ses-20151217_acq-ax_chunk-3_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m362157/ses-20190913/anat/sub-m362157_ses-20190913_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Brain stem
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m358902/ses-20110406/anat/sub-m358902_ses-20110406_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m701054/ses-20141201/anat/sub-m701054_ses-20141201_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m425924/ses-20180712/anat/sub-m425924_ses-20180712_acq-ax_chunk-4_T2w_lesion-manual.nii.gz # Ok
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m002126/ses-20100716/anat/sub-m002126_ses-20100716_acq-ax_chunk-1_T2w_lesion-manual.nii.gz # Brain stem
- bavaria-quebec-spine-ms-unstitched/derivatives/labels/sub-m002126/ses-20100716/anat/sub-m002126_ses-20100716_acq-ax_chunk-2_T2w_lesion-manual.nii.gz # Ok
- canproco/derivatives/labels/sub-mon198/ses-M0/anat/sub-mon198_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon034/ses-M0/anat/sub-mon034_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon211/ses-M0/anat/sub-mon211_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-tor010/ses-M0/anat/sub-tor010_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon118/ses-M0/anat/sub-mon118_ses-M0_PSIR_lesion-manual.nii.gz # Motion artifacts
- canproco/derivatives/labels/sub-cal158/ses-M0/anat/sub-cal158_ses-M0_STIR_lesion-manual.nii.gz # Lesion outside the spinal cord
- canproco/derivatives/labels/sub-mon050/ses-M0/anat/sub-mon050_ses-M0_PSIR_lesion-manual.nii.gz # Motion artifacts
- canproco/derivatives/labels/sub-cal152/ses-M0/anat/sub-cal152_ses-M0_STIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-edm019/ses-M0/anat/sub-edm019_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-tor128/ses-M0/anat/sub-tor128_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon168/ses-M0/anat/sub-mon168_ses-M0_PSIR_lesion-manual.nii.gz # Motion artifact
- canproco/derivatives/labels/sub-cal167/ses-M0/anat/sub-cal167_ses-M0_STIR_lesion-manual.nii.gz # Ok
- canproco/derivatives/labels/sub-edm107/ses-M0/anat/sub-edm107_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon092/ses-M0/anat/sub-mon092_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem and motion artifacts
- canproco/derivatives/labels/sub-edm038/ses-M0/anat/sub-edm038_ses-M0_PSIR_lesion-manual.nii.gz # Lesion in the brain
- canproco/derivatives/labels/sub-mon191/ses-M0/anat/sub-mon191_ses-M0_PSIR_lesion-manual.nii.gz # Motion artifacts
- canproco/derivatives/labels/sub-cal114/ses-M0/anat/sub-cal114_ses-M0_STIR_lesion-manual.nii.gz # Ok
- canproco/derivatives/labels/sub-cal156/ses-M0/anat/sub-cal156_ses-M0_STIR_lesion-manual.nii.gz # Ok
- canproco/derivatives/labels/sub-edm173/ses-M0/anat/sub-edm173_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-tor035/ses-M0/anat/sub-tor035_ses-M0_PSIR_lesion-manual.nii.gz # Ok
- canproco/derivatives/labels/sub-tor070/ses-M0/anat/sub-tor070_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-cal094/ses-M0/anat/sub-cal094_ses-M0_STIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon148/ses-M0/anat/sub-mon148_ses-M0_PSIR_lesion-manual.nii.gz # Motion artifact
- canproco/derivatives/labels/sub-cal130/ses-M0/anat/sub-cal130_ses-M0_STIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-van111/ses-M0/anat/sub-van111_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-cal154/ses-M0/anat/sub-cal154_ses-M0_STIR_lesion-manual.nii.gz # Ok
- canproco/derivatives/labels/sub-mon113/ses-M0/anat/sub-mon113_ses-M0_PSIR_lesion-manual.nii.gz # Motion artifacts
- canproco/derivatives/labels/sub-mon119/ses-M0/anat/sub-mon119_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem and motion artifacts
- canproco/derivatives/labels/sub-van206/ses-M0/anat/sub-van206_ses-M0_PSIR_lesion-manual.nii.gz # Motion artifacts
- canproco/derivatives/labels/sub-mon193/ses-M0/anat/sub-mon193_ses-M0_PSIR_lesion-manual.nii.gz # Ok
- canproco/derivatives/labels/sub-mon138/ses-M0/anat/sub-mon138_ses-M0_PSIR_lesion-manual.nii.gz # Motion artifacts
- canproco/derivatives/labels/sub-tor049/ses-M0/anat/sub-tor049_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon141/ses-M0/anat/sub-mon141_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-cal192/ses-M0/anat/sub-cal192_ses-M0_STIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-edm161/ses-M0/anat/sub-edm161_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon160/ses-M0/anat/sub-mon160_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-tor012/ses-M12/anat/sub-tor012_ses-M12_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-mon079/ses-M0/anat/sub-mon079_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-cal149/ses-M0/anat/sub-cal149_ses-M0_STIR_lesion-manual.nii.gz # Brain stem
- canproco/derivatives/labels/sub-edm078/ses-M0/anat/sub-edm078_ses-M0_PSIR_lesion-manual.nii.gz # Brain stem
- ms-basel-2018/derivatives/labels/sub-5505/ses-20180903/anat/sub-5505_ses-20180903_acq-sagTse_T2w_lesion-manual.nii.gz # Segmentation to be corrected: too much segmented
- ms-basel-2020/derivatives/labels/sub-013/ses-20170607/anat/sub-013_ses-20170607_acq-sagCervTSE_PD_lesion-manual.nii.gz # I don't see the lesions
- ms-basel-2020/derivatives/labels/sub-013/ses-20170607/anat/sub-013_ses-20170607_acq-sagThorTSE_PD_lesion-manual.nii.gz # I don"t see the lesions
- ms-basel-2020/derivatives/labels/sub-007/ses-20170103/anat/sub-007_ses-20170103_acq-sagThorTSE_PD_lesion-manual.nii.gz # I don"t see the lesions
- ms-basel-2020/derivatives/labels/sub-014/ses-20200116/anat/sub-014_ses-20200116_acq-sagThorTSE_PD_lesion-manual.nii.gz # I don"t see the lesions
- ms-basel-2020/derivatives/labels/sub-010/ses-20180918/anat/sub-010_ses-20180918_acq-sagThorTSE_PD_lesion-manual.nii.gz # I don"t see the lesions
- ms-basel-2020/derivatives/labels/sub-010/ses-20180918/anat/sub-010_ses-20180918_acq-sagCervTSE_PD_lesion-manual.nii.gz # Brain stem 
- ms-basel-2020/derivatives/labels/sub-003/ses-20190302/anat/sub-003_ses-20190302_acq-sagThorTSE_run-1_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-009/ses-20180627/anat/sub-009_ses-20180627_acq-sagCervTSE_PD_lesion-manual.nii.gz # Brain stem
- ms-basel-2020/derivatives/labels/sub-004/ses-20170209/anat/sub-004_ses-20170209_acq-sagThorTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-004/ses-20170209/anat/sub-004_ses-20170209_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-015/ses-20200128/anat/sub-015_ses-20200128_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-015/ses-20200128/anat/sub-015_ses-20200128_acq-sagThorTSE_run-1_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-006/ses-20180814/anat/sub-006_ses-20180814_acq-sagCervTSE_PD_lesion-manual.nii.gz # Brain stem
- ms-basel-2020/derivatives/labels/sub-001/ses-20170622/anat/sub-001_ses-20170622_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-012/ses-20170710/anat/sub-012_ses-20170710_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-012/ses-20170710/anat/sub-012_ses-20170710_acq-sagThorTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-016/ses-20180117/anat/sub-016_ses-20180117_acq-sagThorTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-016/ses-20180117/anat/sub-016_ses-20180117_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-005/ses-20180417/anat/sub-005_ses-20180417_acq-sagThorTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-005/ses-20180417/anat/sub-005_ses-20180417_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-008/ses-20180222/anat/sub-008_ses-20180222_acq-sagThorTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-008/ses-20180222/anat/sub-008_ses-20180222_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-002/ses-20190325/anat/sub-002_ses-20190325_acq-sagThorTSE_run-2_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-002/ses-20190325/anat/sub-002_ses-20190325_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-basel-2020/derivatives/labels/sub-011/ses-20170131/anat/sub-011_ses-20170131_acq-sagCervTSE_PD_lesion-manual.nii.gz # Ok
- ms-karolinska-2020/derivatives/labels/sub-2038/ses-M0/anat/sub-2038_ses-M0_acq-ax_echo-1_MEGRE_lesion-manual.nii.gz # Ok
- ms-nyu/derivatives/labels/sub-119/anat/sub-119_acq-sagSup_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- ms-nyu/derivatives/labels/sub-138/anat/sub-138_acq-sagSup_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- ms-nyu/derivatives/labels/sub-148/anat/sub-148_acq-sagSup_T2w_lesion-manual.nii.gz # Brain stem
- ms-nyu/derivatives/labels/sub-114/anat/sub-114_acq-sagSup_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- ms-nyu/derivatives/labels/sub-155/anat/sub-155_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- ms-nyu/derivatives/labels/sub-122/anat/sub-122_acq-sagSup_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- ms-nyu/derivatives/labels/sub-036/anat/sub-036_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- ms-nyu/derivatives/labels/sub-146/anat/sub-146_acq-sagSup_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- ms-nyu/derivatives/labels/sub-139/anat/sub-139_acq-sag_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- ms-nyu/derivatives/labels/sub-120/anat/sub-120_acq-sagSup_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- ms-nyu/derivatives/labels/sub-120/anat/sub-120_acq-axInf_T2w_lesion-manual.nii.gz # Ok
- ms-nyu/derivatives/labels/sub-112/anat/sub-112_acq-sagSup_T2w_lesion-manual.nii.gz # Brain stem
- ms-nyu/derivatives/labels/sub-161/anat/sub-161_acq-sagSup_T2w_lesion-manual.nii.gz # Brain stem
- ms-nyu/derivatives/labels/sub-137/anat/sub-137_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- ms-nyu/derivatives/labels/sub-130/anat/sub-130_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- ms-nyu/derivatives/labels/sub-123/anat/sub-123_acq-sagSup_T2w_lesion-manual.nii.gz # Brain stem
- nih-ms-mp2rage/derivatives/labels/sub-nih069/anat/sub-nih069_UNIT1_desc-rater1_label-lesion_seg.nii.gz # Brain stem
- nih-ms-mp2rage/derivatives/labels/sub-nih138/anat/sub-nih138_UNIT1_desc-rater1_label-lesion_seg.nii.gz # Brain stem
- nih-ms-mp2rage/derivatives/labels/sub-nih169/anat/sub-nih169_UNIT1_desc-rater1_label-lesion_seg.nii.gz # Brain stem
- nih-ms-mp2rage/derivatives/labels/sub-nih081/anat/sub-nih081_UNIT1_desc-rater1_label-lesion_seg.nii.gz # Brain stem
- nih-ms-mp2rage/derivatives/labels/sub-nih150/anat/sub-nih150_UNIT1_desc-rater1_label-lesion_seg.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-bwh055/anat/sub-bwh055_acq-sag_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-milanFilippi111/anat/sub-milanFilippi111_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd139/anat/sub-nyuShepherd139_acq-sag_T2w_lesion-manual.nii.gz # Lesion outside spinal cord
- sct-testing-large/derivatives/labels/sub-lyonOfsep004/anat/sub-lyonOfsep004_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd112/anat/sub-nyuShepherd112_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nihReich013/anat/sub-nihReich013_acq-sag_T2w_lesion-manual.nii.gz #Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi040/anat/sub-milanFilippi040_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nihReich014/anat/sub-nihReich014_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi105/anat/sub-milanFilippi105_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-karoTobiasMS003/ses-01/anat/sub-karoTobiasMS003_ses-01_T2star_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd115/anat/sub-nyuShepherd115_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nihReich026/anat/sub-nihReich026_T2star_lesion-manual.nii.gz # Lesion outside the body
- sct-testing-large/derivatives/labels/sub-bwh017/anat/sub-bwh017_acq-sagstir_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-vanderbiltSeth012/anat/sub-vanderbiltSeth012_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-bwh025/anat/sub-bwh025_acq-ax_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-bwh025/anat/sub-bwh025_acq-sagstir_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-vanderbiltSeth020/anat/sub-vanderbiltSeth020_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi112/anat/sub-milanFilippi112_acq-sag_T2w_lesion-manual.nii.gz # Brain stem # Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi068/anat/sub-milanFilippi068_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-bwh056/anat/sub-bwh056_acq-sagstir_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-karoTobiasMS014/ses-01/anat/sub-karoTobiasMS014_ses-01_T2star_lesion-manual.nii.gz # Ok
- sct-testing-large/derivatives/labels/sub-nyuShepherd130/anat/sub-nyuShepherd130_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nihReich022/anat/sub-nihReich022_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi034/anat/sub-milanFilippi034_acq-ax_T2star_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-nyuShepherd154/anat/sub-nyuShepherd154_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd123/anat/sub-nyuShepherd123_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-montpellierLesion006/anat/sub-montpellierLesion006_acq-inf_T2star_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-nihReich017/anat/sub-nihReich017_T2star_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-nyuShepherd116/anat/sub-nyuShepherd116_acq-sag_T2w_lesion-manual.nii.gz  # Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi076/anat/sub-milanFilippi076_acq-sag_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-karoTobiasMS021/ses-01/anat/sub-karoTobiasMS021_ses-01_T2star_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-nyuShepherd105/anat/sub-nyuShepherd105_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-bwh061/anat/sub-bwh061_acq-ax_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-montpellierLesion010/anat/sub-montpellierLesion010_acq-sagcerv_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-nyuShepherd148/anat/sub-nyuShepherd148_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd107/anat/sub-nyuShepherd107_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-amuVirginie020/anat/sub-amuVirginie020_acq-sup_T2star_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-karoTobiasMS030/ses-01/anat/sub-karoTobiasMS030_ses-01_T2star_lesion-manual.nii.gz # Mini lesions in the spinal cord should be removed
- sct-testing-large/derivatives/labels/sub-lyonOfsep082/anat/sub-lyonOfsep082_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nihReich020/anat/sub-nihReich020_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd113/anat/sub-nyuShepherd113_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd113/anat/sub-nyuShepherd113_acq-inf_T2w_lesion-manual.nii.gz # Ok
- sct-testing-large/derivatives/labels/sub-ucsfTalbott010/anat/sub-ucsfTalbott010_acq-ax_T2w_lesion-manual.nii.gz # Ok
- sct-testing-large/derivatives/labels/sub-nihReich033/anat/sub-nihReich033_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd132/anat/sub-nyuShepherd132_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd035/anat/sub-nyuShepherd035_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi058/anat/sub-milanFilippi058_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi058/anat/sub-milanFilippi058_acq-ax_T2star_lesion-manual.nii.gz # Ok
- sct-testing-large/derivatives/labels/sub-milanFilippi025/anat/sub-milanFilippi025_acq-ax_T2star_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-bwh011/anat/sub-bwh011_acq-sagstir_T2w_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-nihReich005/anat/sub-nihReich005_T2star_lesion-manual.nii.gz # Brain stem and motion artifacts
- sct-testing-large/derivatives/labels/sub-nyuShepherd141/anat/sub-nyuShepherd141_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-vanderbiltSeth003/anat/sub-vanderbiltSeth003_T2star_lesion-manual.nii.gz # Motion artifacts
- sct-testing-large/derivatives/labels/sub-nihReich016/anat/sub-nihReich016_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-karoTobiasMS033/ses-01/anat/sub-karoTobiasMS033_ses-01_T2star_lesion-manual.nii.gz # Small lesions to remove
- sct-testing-large/derivatives/labels/sub-karoTobiasMS001/ses-01/anat/sub-karoTobiasMS001_ses-01_T2star_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-milanFilippi099/anat/sub-milanFilippi099_acq-ax_T2star_lesion-manual.nii.gz # Lesion outside the spinal cord
- sct-testing-large/derivatives/labels/sub-milanFilippi007/anat/sub-milanFilippi007_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nihReich011/anat/sub-nihReich011_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-milanFilippi087/anat/sub-milanFilippi087_acq-sag_T2w_lesion-manual.nii.gz # Brain stem
- sct-testing-large/derivatives/labels/sub-nyuShepherd131/anat/sub-nyuShepherd131_acq-sag_T2w_lesion-manual.nii.gz # Brain stem

From this, the following work must be done:

• Correct images which have lesions segmented outside of the spinal cord
• Create copies of the lesion segmentation in folder /derivatives/labels-sc-ms-lesion-seg
• Remove lesions in the brain stem

[plbenveniste]

We decided to discard the PDw images as the lesions are very hard to discern on this contrast and not commonly used in MS imaging.

[plbenveniste]

The corrections were done in every dataset.
Except for ms-basel-2018 and ms-basel-2020 (because they only had SC lesions), I created a folder labels-ms-spinal-cord-only.
I just need to correct the following images in the labels folder which have segmentations outside the CNS for most and very small lesions segmented for others:

• sub-nihReich026_T2star_lesion-manual.nii.gz
• sub-bwh056_acq-sagstir_T2w_lesion-manual.nii.gz
• sub-montpellierLesion006_acq-inf_T2star_lesion-manual.nii.gz
• sub-montpellierLesion006_acq-inf_T2star_lesion-manual.nii.gz
• sub-milanFilippi034_acq-ax_T2star_lesion-manual.nii.gz
• sub-milanFilippi076_acq-sag_T2w_lesion-manual.nii.gz
• sub-karoTobiasMS021_ses-01_T2star_lesion-manual.nii.gz
• sub-bwh061_acq-ax_T2w_lesion-manual.nii.gz
• sub-bwh061_acq-ax_T2w_lesion-manual.nii.gz
• sub-amuVirginie020_acq-sup_T2star_lesion-manual.nii.gz
• sub-karoTobiasMS030_ses-01_T2star_lesion-manual.nii.gz
• sub-milanFilippi025_acq-ax_T2star_lesion-manual.nii.gz
• sub-bwh011_acq-sagstir_T2w_lesion-manual.nii.gz
• sub-karoTobiasMS033_ses-01_T2star_lesion-manual.nii.gz
• sub-karoTobiasMS001_ses-01_T2star_lesion-manual.nii.gz
• sub-milanFilippi099_acq-ax_T2star_lesion-manual.nii.gz

[plbenveniste]

While working on this, I realized that the subjects in ms-nyu were in sct-testing-large. This was investigated in #44.

[plbenveniste]

TODO:

• correct the images listed in comment above: QC of datasets #40 (comment)