I wonder what information we can rely on to ensure the order of images in each series. Firstly, I have used filename convention, but after googling for awhile, it's not the DICOM standard to use the filename to order images.
\nI've noticed InstanceNumber info as well. Though DICOM standard lists this tag as Type 2: \"Required, Empty if Unknown\", I've checked the training data and seen no missing data in this field.
\nCan we be sure that this information is readily available in the private test as well ?
@cdcarr , can you answer this ?
", "messages": [ { "id": "1485726", "postDate": "08/22/2021 11:18:58", "content": "I wonder what information we can rely on to ensure the order of images in each series. Firstly, I have used filename convention, but after googling for awhile, it's not the DICOM standard to use the filename to order images.
\nI've noticed InstanceNumber info as well. Though DICOM standard lists this tag as Type 2: \"Required, Empty if Unknown\", I've checked the training data and seen no missing data in this field.
\nCan we be sure that this information is readily available in the private test as well ?
@cdcarr , can you answer this ?
", "rawMarkdown": "I wonder what information we can rely on to ensure the order of images in each series. Firstly, I have used filename convention, but after googling for awhile, it's not the DICOM standard to use the filename to order images. \nI've noticed InstanceNumber info as well. Though DICOM standard lists this tag as Type 2: \"Required, Empty if Unknown\", I've checked the training data and seen no missing data in this field. \nCan we be sure that this information is readily available in the private test as well ?\n\n@cdcarr , can you answer this ?", "votes": null }, { "id": "1485831", "postDate": "08/22/2021 13:05:10", "content": "You shouldn't use the instance number to order images. It may not always be accurate, and as you noted, it's a required tag, but can be empty or out of order. Likewise there is another tag (SliceLocation 0020,1041) that can be used, but it is optional and may not be present at all.
\nThe correct way to order slices is to use the ImagePositionPatient (0020,0032) and ImageOrientationPatient (0020,0037) to calculate the orientation and location.
", "rawMarkdown": "You shouldn't use the instance number to order images. It may not always be accurate, and as you noted, it's a required tag, but can be empty or out of order. Likewise there is another tag (SliceLocation 0020,1041) that can be used, but it is optional and may not be present at all.\n\nThe correct way to order slices is to use the ImagePositionPatient (0020,0032) and ImageOrientationPatient (0020,0037) to calculate the orientation and location.", "votes": null }, { "id": "1487948", "postDate": "08/24/2021 01:43:11", "content": "Can you answer this ? @ujjwalbaid
", "rawMarkdown": "Can you answer this ? @ujjwalbaid", "votes": null }, { "id": "1489624", "postDate": "08/25/2021 06:27:18", "content": "I found this example handy for accessing the slices and ordering…
\nhttps://pydicom.github.io/pydicom/stable/auto_examples/image_processing/reslice.html#sphx-glr-auto-examples-image-processing-reslice-py
The example you've given uses SliceLocation as the ordering information. In DICOM standard, this attribute is optional. Relying on this tag seems to be risky.
", "rawMarkdown": "The example you've given uses SliceLocation as the ordering information. In DICOM standard, this attribute is optional. Relying on this tag seems to be risky.", "votes": null }, { "id": "1490001", "postDate": "08/25/2021 12:39:37", "content": "Here's a notebook I made that uses ImagePositionPatient to sort slice order -> https://www.kaggle.com/davidbroberts/determining-dicom-image-order
", "rawMarkdown": "Here's a notebook I made that uses ImagePositionPatient to sort slice order -> https://www.kaggle.com/davidbroberts/determining-dicom-image-order", "votes": null } ], "comments": [ { "id": 1485831, "author_name": "davidbroberts", "author_url": "", "post_date": "08/22/2021 13:05:10", "content": "You shouldn't use the instance number to order images. It may not always be accurate, and as you noted, it's a required tag, but can be empty or out of order. Likewise there is another tag (SliceLocation 0020,1041) that can be used, but it is optional and may not be present at all.
\nThe correct way to order slices is to use the ImagePositionPatient (0020,0032) and ImageOrientationPatient (0020,0037) to calculate the orientation and location.
", "votes": null, "replies": [] }, { "id": 1487948, "author_name": "namgalielei", "author_url": "", "post_date": "08/24/2021 01:43:11", "content": "Can you answer this ? @ujjwalbaid
", "votes": null, "replies": [] }, { "id": 1489624, "author_name": "adamwigg", "author_url": "", "post_date": "08/25/2021 06:27:18", "content": "I found this example handy for accessing the slices and ordering…
\nhttps://pydicom.github.io/pydicom/stable/auto_examples/image_processing/reslice.html#sphx-glr-auto-examples-image-processing-reslice-py
The example you've given uses SliceLocation as the ordering information. In DICOM standard, this attribute is optional. Relying on this tag seems to be risky.
", "votes": null, "replies": [] } ] }, { "id": 1490001, "author_name": "davidbroberts", "author_url": "", "post_date": "08/25/2021 12:39:37", "content": "Here's a notebook I made that uses ImagePositionPatient to sort slice order -> https://www.kaggle.com/davidbroberts/determining-dicom-image-order
", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "1485726": "I wonder what information we can rely on to ensure the order of images in each series. Firstly, I have used filename convention, but after googling for awhile, it's not the DICOM standard to use the filename to order images. \nI've noticed InstanceNumber info as well. Though DICOM standard lists this tag as Type 2: \"Required, Empty if Unknown\", I've checked the training data and seen no missing data in this field. \nCan we be sure that this information is readily available in the private test as well ?\n\n@cdcarr , can you answer this ?", "1485831": "You shouldn't use the instance number to order images. It may not always be accurate, and as you noted, it's a required tag, but can be empty or out of order. Likewise there is another tag (SliceLocation 0020,1041) that can be used, but it is optional and may not be present at all.\n\nThe correct way to order slices is to use the ImagePositionPatient (0020,0032) and ImageOrientationPatient (0020,0037) to calculate the orientation and location.", "1487948": "Can you answer this ? @ujjwalbaid", "1489624": "I found this example handy for accessing the slices and ordering...\nhttps://pydicom.github.io/pydicom/stable/auto_examples/image_processing/reslice.html#sphx-glr-auto-examples-image-processing-reslice-py", "1489735": "The example you've given uses SliceLocation as the ordering information. In DICOM standard, this attribute is optional. Relying on this tag seems to be risky.", "1490001": "Here's a notebook I made that uses ImagePositionPatient to sort slice order -> https://www.kaggle.com/davidbroberts/determining-dicom-image-order" }, "source": "meta" }