Add the whole-spine dataset

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 [email protected]: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

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',