From 0d19c506de4338c8ab4b87167bffce5c4fd6cb85 Mon Sep 17 00:00:00 2001 From: valosekj Date: Thu, 28 Mar 2024 12:26:43 -0400 Subject: [PATCH] Add the `whole-spine` dataset --- dataset-conversion/README.md | 10 ++++++++++ dataset-conversion/create_msd_data.py | 2 ++ 2 files changed, 12 insertions(+) diff --git a/dataset-conversion/README.md b/dataset-conversion/README.md index 3eea04f..75aeafa 100644 --- a/dataset-conversion/README.md +++ b/dataset-conversion/README.md @@ -18,6 +18,15 @@ git annex get $(find . -name "*space-other_T2w.nii.gz") git annex get $(find . -name "*space-other_T2w_label-SC_seg.nii.gz") ``` +`whole-spine` (n=45) + +```commandline +git clone git@data.neuro.polymtl.ca:datasets/whole-spine +cd whole-spine +git annex dead here +git annex get $(find . -name "*T2w.nii.gz") +git annex get $(find . -name "*T2w_seg.nii.gz") +``` `canproco` (n=413) @@ -63,6 +72,7 @@ git annex get $(find . -name "*T2w_seg.nii.gz") ```commandline python /Users/user/code/model-seg-dcm/vit_unetr_ssl/create_msd_data.py --path-data data-multi-subject --dataset-name spine-generic --path-out . --split 0.8 0.2 --seed 42 +python /Users/user/code/model-seg-dcm/vit_unetr_ssl/create_msd_data.py --path-data whole-spine --dataset-name whole-spine --path-out . --split 0.8 0.2 --seed 42 python /Users/user/code/model-seg-dcm/vit_unetr_ssl/create_msd_data.py --path-data canproco --dataset-name canproco --path-out . --split 0.8 0.2 --seed 42 python /Users/user/code/model-seg-dcm/vit_unetr_ssl/create_msd_data.py --path-data sci-colorado --dataset-name sci-colorado --path-out . --split 0.8 0.2 --seed 42 python /Users/user/code/model-seg-dcm/vit_unetr_ssl/create_msd_data.py --path-data dcm-zurich --dataset-name dcm-zurich --path-out . --split 0.8 0.2 --seed 42 diff --git a/dataset-conversion/create_msd_data.py b/dataset-conversion/create_msd_data.py index 56fea62..a66fa23 100644 --- a/dataset-conversion/create_msd_data.py +++ b/dataset-conversion/create_msd_data.py @@ -28,6 +28,7 @@ contrast_dict = { 'spine-generic': 'space-other_T2w', # iso T2w (preprocessed data) + 'whole-spine': 'T2w', # iso T2w 'canproco': 'ses-M0_T2w', # iso T2w (session M0) 'dcm-zurich': 'acq-axial_T2w', # axial T2w 'sci-paris': 'T2w', # iso T2w @@ -37,6 +38,7 @@ # Spinal cord segmentation file suffixes for different datasets sc_fname_suffix_dict = { 'spine-generic': 'label-SC_seg', + 'whole-spine': 'seg', 'canproco': 'seg-manual', 'dcm-zurich': 'label-SC_mask-manual', 'sci-paris': 'seg-manual',