Sergey Kuznetsov commited on
Commit
4db5532
1 Parent(s): eef4141

First version of the IXI2D dataset

Browse files
Files changed (6) hide show
  1. .gitattributes +2 -0
  2. .gitignore +3 -0
  3. README.md +117 -0
  4. data/train.zip +3 -0
  5. data/valid.zip +3 -0
  6. ixi2d.py +65 -0
.gitattributes CHANGED
@@ -53,3 +53,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
53
  *.jpg filter=lfs diff=lfs merge=lfs -text
54
  *.jpeg filter=lfs diff=lfs merge=lfs -text
55
  *.webp filter=lfs diff=lfs merge=lfs -text
 
 
 
53
  *.jpg filter=lfs diff=lfs merge=lfs -text
54
  *.jpeg filter=lfs diff=lfs merge=lfs -text
55
  *.webp filter=lfs diff=lfs merge=lfs -text
56
+ data/train.zip filter=lfs diff=lfs merge=lfs -text
57
+ data/valid.zip filter=lfs diff=lfs merge=lfs -text
.gitignore ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ __pycache__/
2
+ .DS_Store
3
+ .idea
README.md ADDED
@@ -0,0 +1,117 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ annotations_creators:
3
+ - no-annotation
4
+ language: []
5
+ language_creators:
6
+ - expert-generated
7
+ license:
8
+ - cc-by-sa-3.0
9
+ multilinguality: []
10
+ pretty_name: IXI-2D
11
+ size_categories:
12
+ - 10K<n<100K
13
+ source_datasets:
14
+ - original
15
+ tags:
16
+ - medical imaging
17
+ - mri
18
+ - brains
19
+ task_categories:
20
+ - unconditional-image-generation
21
+ task_ids: []
22
+ dataset_info:
23
+ features:
24
+ - name: image
25
+ dtype: image
26
+ splits:
27
+ - name: train
28
+ num_bytes: 111340223
29
+ num_examples: 25447
30
+ - name: validation
31
+ num_bytes: 12463820
32
+ num_examples: 2828
33
+ download_size: 133058419
34
+ dataset_size: 123804043
35
+ ---
36
+
37
+ # Dataset Card for IXI2D
38
+
39
+ ### Dataset Summary
40
+
41
+ This IXI2D dataset contains around 28000 2D slices extracted from 600 MRI images of healthy subjects. Each MRI volume was skull-stripped, white matter normalized and registered to the *'fsaverage'* template using affine transformation.
42
+
43
+ ## Dataset Structure
44
+
45
+ ### Data Instances
46
+
47
+ [More Information Needed]
48
+
49
+ ### Data Fields
50
+
51
+ [More Information Needed]
52
+
53
+ ### Data Splits
54
+
55
+ [More Information Needed]
56
+
57
+ ## Dataset Creation
58
+
59
+ ### Curation Rationale
60
+
61
+ [More Information Needed]
62
+
63
+ ### Source Data
64
+
65
+ #### Initial Data Collection and Normalization
66
+
67
+ [More Information Needed]
68
+
69
+ #### Who are the source language producers?
70
+
71
+ [More Information Needed]
72
+
73
+ ### Annotations
74
+
75
+ #### Annotation process
76
+
77
+ [More Information Needed]
78
+
79
+ #### Who are the annotators?
80
+
81
+ [More Information Needed]
82
+
83
+ ### Personal and Sensitive Information
84
+
85
+ [More Information Needed]
86
+
87
+ ## Considerations for Using the Data
88
+
89
+ ### Social Impact of Dataset
90
+
91
+ [More Information Needed]
92
+
93
+ ### Discussion of Biases
94
+
95
+ [More Information Needed]
96
+
97
+ ### Other Known Limitations
98
+
99
+ [More Information Needed]
100
+
101
+ ## Additional Information
102
+
103
+ ### Dataset Curators
104
+
105
+ [More Information Needed]
106
+
107
+ ### Licensing Information
108
+
109
+ [More Information Needed]
110
+
111
+ ### Citation Information
112
+
113
+ [More Information Needed]
114
+
115
+ ### Contributions
116
+
117
+ Thanks to [@iamkzntsv](https://github.com/iamkzntsv) for adding this dataset.
data/train.zip ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d55cd05eda000426dec632d2e0f4af3fcd20c141fa4f035eb37af0b0e8c31dba
3
+ size 119677698
data/valid.zip ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2ec4bf194ce7d94b206922596c3d43e26f9eefa31bdc4d457c5f74a37a8c9a0d
3
+ size 13380721
ixi2d.py ADDED
@@ -0,0 +1,65 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ import datasets
2
+
3
+ logger = datasets.logging.get_logger(__name__)
4
+
5
+ _HOMEPAGE = 'https://brain-development.org/ixi-dataset/'
6
+
7
+ _DESCRIPTION = (
8
+ "This dataset contains around 28000 2D slices extracted from 600 MRI images of healthy subjects."
9
+ " Each MRI volume was skull-stripped, white matter normalized and registered to the 'fsaverage' template using affine transformation. "
10
+ )
11
+
12
+ _URLS = {
13
+ 'train': 'data/train.zip',
14
+ 'valid': 'data/valid.zip'
15
+ }
16
+
17
+ _LICENSE = """\
18
+ LICENSE AGREEMENT
19
+ =================
20
+ - The IXI-2D dataset consists of images from IXI Dataset [1] which are
21
+ property of the Biomedical Image Analysis Group, Imperial College London. Any use beyond
22
+ scientific fair use must be negotiated with the respective picture owners
23
+ according to the Creative Commons license [2].
24
+ [1] https://brain-development.org/ixi-dataset/
25
+ [2] https://creativecommons.org/licenses/by-sa/3.0/legalcode
26
+ """
27
+
28
+
29
+ class IXI2D(datasets.GeneratorBasedBuilder):
30
+ """Food-101 Images dataset"""
31
+
32
+ def _info(self):
33
+ return datasets.DatasetInfo(
34
+ features=datasets.Features(
35
+ {
36
+ "image": datasets.Image(),
37
+ }
38
+ ),
39
+ homepage=_HOMEPAGE,
40
+ description=_DESCRIPTION,
41
+ license=_LICENSE
42
+ )
43
+
44
+ def _split_generators(self, dl_manager):
45
+ archive_path = dl_manager.download(_URLS)
46
+ return [
47
+ datasets.SplitGenerator(
48
+ name=datasets.Split.TRAIN,
49
+ gen_kwargs={
50
+ "images": dl_manager.iter_archive(archive_path['train']),
51
+ },
52
+ ),
53
+ datasets.SplitGenerator(
54
+ name=datasets.Split.VALIDATION,
55
+ gen_kwargs={
56
+ "images": dl_manager.iter_archive(archive_path['valid']),
57
+ },
58
+ ),
59
+ ]
60
+
61
+ def _generate_examples(self, images):
62
+ for file_path, file_obj in images:
63
+ yield file_path, {
64
+ "image": {"path": file_path, "bytes": file_obj.read()},
65
+ }