{ "id": 186660, "title": "Simple ITK Error", "url": "/competitions/rsna-str-pulmonary-embolism-detection/discussion/186660", "author_name": "Catadanna", "post_date": "2020-09-25T12:22:55.712000", "votes": 3, "comment_count": 16, "views": 0, "content": "

Did someone have problems reading images with Simple ITK ?

\n

I get this error :

\n
\n

RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:107:
\n sitk::ERROR: Unable to determine ImageIO reader for \"/kaggle/input/rsna-str-pulmonary-embolism-detection/train/b35a5a9787a6/e6e025707e2f/1b058f972dec.dcm\"

\n
\n

I even asked directly on Github but they say it works, it might come from some restrictions in Kaggle.

\n

Any help will be appreciated.

", "messages": [ { "id": 1026573, "postDate": "2020-09-25T12:22:55.713Z", "content": "

Did someone have problems reading images with Simple ITK ?

\n

I get this error :

\n
\n

RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:107:
\n sitk::ERROR: Unable to determine ImageIO reader for \"/kaggle/input/rsna-str-pulmonary-embolism-detection/train/b35a5a9787a6/e6e025707e2f/1b058f972dec.dcm\"

\n
\n

I even asked directly on Github but they say it works, it might come from some restrictions in Kaggle.

\n

Any help will be appreciated.

", "rawMarkdown": "Did someone have problems reading images with Simple ITK ? \n\nI get this error : \n\n> RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:107:\nsitk::ERROR: Unable to determine ImageIO reader for \"/kaggle/input/rsna-str-pulmonary-embolism-detection/train/b35a5a9787a6/e6e025707e2f/1b058f972dec.dcm\"\n\nI even asked directly on Github but they say it works, it might come from some restrictions in Kaggle. \n\nAny help will be appreciated.\n", "votes": 3 }, { "id": 1027952, "postDate": "2020-09-26T13:42:12.310Z", "content": "

Good job, continue like this ! BRAVO

", "rawMarkdown": "Good job, continue like this ! BRAVO ", "votes": -4, "replies": [ { "id": 1027971, "postDate": "2020-09-26T13:45:12.760Z", "content": "

What do you mean? The problem is I cannot continue because of this issue.

", "rawMarkdown": "What do you mean? The problem is I cannot continue because of this issue." }, { "id": 1027982, "postDate": "2020-09-26T13:56:16.370Z", "content": "

@catadanna the message above is spam (It's a bot that sends messages to be upvoted)

\n

Sorry I can't help with TK. as I don't use it

", "rawMarkdown": "@catadanna the message above is spam (It's a bot that sends messages to be upvoted) \n\nSorry I can't help with TK. as I don't use it", "votes": 1 } ] }, { "id": 1028030, "postDate": "2020-09-26T14:40:00.420Z", "content": "

That file you listed is not one of the files that pydicom needs GDCM for. So that is probably unrelated.

\n

Is that the only file you have trouble with, or are you getting errors on all your files?

", "rawMarkdown": "That file you listed is not one of the files that pydicom needs GDCM for. So that is probably unrelated.\n\nIs that the only file you have trouble with, or are you getting errors on all your files?", "replies": [ { "id": 1028038, "postDate": "2020-09-26T14:44:41.847Z", "content": "

This topic is not about the GDCM issue but the problem with Simple ITK reading a dicom file. Someone mentioned GDCM but I answered it is not about that.

\n

Now, to answer the question : this is the first file I tried to parse with Simple ITK, I tried with other files and the problem is the same. It might be a general problem. I changed the ITK version and I got the same thing.

", "rawMarkdown": "This topic is not about the GDCM issue but the problem with Simple ITK reading a dicom file. Someone mentioned GDCM but I answered it is not about that.\n\nNow, to answer the question : this is the first file I tried to parse with Simple ITK, I tried with other files and the problem is the same. It might be a general problem. I changed the ITK version and I got the same thing. ", "replies": [ { "id": 1028133, "postDate": "2020-09-26T16:06:51.947Z", "content": "

I'm able to read an image from the Pulmonary Fibrosis dataset with Simple ITK. So, my thought is either the pixel format is not supported or that SimpleITK needs a Dicom tag that has been removed/anonymized.

", "rawMarkdown": "I'm able to read an image from the Pulmonary Fibrosis dataset with Simple ITK. So, my thought is either the pixel format is not supported or that SimpleITK needs a Dicom tag that has been removed/anonymized. " }, { "id": 1028433, "postDate": "2020-09-26T20:55:14.387Z", "content": "

Did you try the image I mentioned?
\nWhere can you read it, in Kaggle the notebook, or on your computer? I did not try on my computer but it seems it works on a computer but not on notebooks.

", "rawMarkdown": "Did you try the image I mentioned? \nWhere can you read it, in Kaggle the notebook, or on your computer? I did not try on my computer but it seems it works on a computer but not on notebooks. " }, { "id": 1028447, "postDate": "2020-09-26T21:18:53.277Z", "content": "

In a Notebook, I failed with Simple ITK on any image in this competition.

\n

But Simple ITK could read images from another competition (Pulmonary Fibrosis). So Simple ITK works, but something about the dataset for this competition is causing it problems.

\n

I'm working with Pydicom, and with the GDCM fix, it seems to read everything fine. I know Simple ITK adds some other functionality.

\n

Good luck,

\n

-Rich

", "rawMarkdown": "In a Notebook, I failed with Simple ITK on any image in this competition.\n\nBut Simple ITK could read images from another competition (Pulmonary Fibrosis). So Simple ITK works, but something about the dataset for this competition is causing it problems.\n\nI'm working with Pydicom, and with the GDCM fix, it seems to read everything fine. I know Simple ITK adds some other functionality.\n\nGood luck,\n\n-Rich" }, { "id": 1028449, "postDate": "2020-09-26T21:23:56.607Z", "content": "

Hallo, thank you for your answer. I know it works in the notebook in the Pulmonary Fibrosis competition, I used it there. There must be a problem with this other competition.

\n

Good luck to you too and thank you again!

", "rawMarkdown": "Hallo, thank you for your answer. I know it works in the notebook in the Pulmonary Fibrosis competition, I used it there. There must be a problem with this other competition. \n\nGood luck to you too and thank you again!" }, { "id": 1028686, "postDate": "2020-09-27T05:41:54.697Z", "content": "

hi @richardepstein, can you explain me the gdcm fix? I'm stuck with that error and I noticed that is not just the train set but also the private test set to have images not readable.
\nSorry, I'm new to machine learning

", "rawMarkdown": "hi @richardepstein, can you explain me the gdcm fix? I'm stuck with that error and I noticed that is not just the train set but also the private test set to have images not readable. \nSorry, I'm new to machine learning " }, { "id": 1028787, "postDate": "2020-09-27T07:55:49.663Z", "content": "

@neuronffh : Just add to your code :

\n
!conda install -c conda-forge gdcm -y\n
\n

Be aware, you need to turn the Internet \"On\" for that.

", "rawMarkdown": "@neuronffh : Just add to your code :\n\n\n```\n!conda install -c conda-forge gdcm -y\n```\n\nBe aware, you need to turn the Internet \"On\" for that." }, { "id": 1028910, "postDate": "2020-09-27T10:09:54.830Z", "content": "

Thank you for the answer!

", "rawMarkdown": "Thank you for the answer!" }, { "id": 1028955, "postDate": "2020-09-27T10:53:57Z", "content": "

https://www.kaggle.com/richardepstein/load-gdcm-in-notebook-without-internet

\n

This notebook let's you load gdcm without internet.

", "rawMarkdown": "https://www.kaggle.com/richardepstein/load-gdcm-in-notebook-without-internet\n\nThis notebook let's you load gdcm without internet. ", "votes": 2 }, { "id": 1029024, "postDate": "2020-09-27T12:09:01.637Z", "content": "

Thank you! It works now

", "rawMarkdown": "Thank you! It works now" } ] } ] }, { "id": 1026976, "postDate": "2020-09-25T17:50:37.923Z", "content": "

I had problems reading some of the .dcm in the train set using pydicom. It gave me
\nRuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM)
\nDon't know if it's related

", "rawMarkdown": "I had problems reading some of the .dcm in the train set using pydicom. It gave me\nRuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM)\nDon't know if it's related", "replies": [ { "id": 1026988, "postDate": "2020-09-25T18:05:01.677Z", "content": "

No, I meant the use of Simple ITK library, precisely, not Pydicom.

", "rawMarkdown": "No, I meant the use of Simple ITK library, precisely, not Pydicom." } ] } ], "comments": [ { "id": 1027952, "author_name": "Naim Mhedhbi", "author_url": "", "post_date": "2020-09-26T13:42:12.310000", "content": "

Good job, continue like this ! BRAVO

", "votes": -4, "replies": [ { "id": 1027971, "author_name": "Catadanna", "author_url": "", "post_date": "2020-09-26T13:45:12.760000", "content": "

What do you mean? The problem is I cannot continue because of this issue.

", "votes": 0, "replies": [] }, { "id": 1027982, "author_name": "yuval reina", "author_url": "", "post_date": "2020-09-26T13:56:16.370000", "content": "

@catadanna the message above is spam (It's a bot that sends messages to be upvoted)

\n

Sorry I can't help with TK. as I don't use it

", "votes": 1, "replies": [] } ] }, { "id": 1028030, "author_name": "quadcore/Richard Epstein", "author_url": "", "post_date": "2020-09-26T14:40:00.420000", "content": "

That file you listed is not one of the files that pydicom needs GDCM for. So that is probably unrelated.

\n

Is that the only file you have trouble with, or are you getting errors on all your files?

", "votes": 0, "replies": [ { "id": 1028038, "author_name": "Catadanna", "author_url": "", "post_date": "2020-09-26T14:44:41.847000", "content": "

This topic is not about the GDCM issue but the problem with Simple ITK reading a dicom file. Someone mentioned GDCM but I answered it is not about that.

\n

Now, to answer the question : this is the first file I tried to parse with Simple ITK, I tried with other files and the problem is the same. It might be a general problem. I changed the ITK version and I got the same thing.

", "votes": 0, "replies": [ { "id": 1028133, "author_name": "quadcore/Richard Epstein", "author_url": "", "post_date": "2020-09-26T16:06:51.947000", "content": "

I'm able to read an image from the Pulmonary Fibrosis dataset with Simple ITK. So, my thought is either the pixel format is not supported or that SimpleITK needs a Dicom tag that has been removed/anonymized.

", "votes": 0, "replies": [] }, { "id": 1028433, "author_name": "Catadanna", "author_url": "", "post_date": "2020-09-26T20:55:14.387000", "content": "

Did you try the image I mentioned?
\nWhere can you read it, in Kaggle the notebook, or on your computer? I did not try on my computer but it seems it works on a computer but not on notebooks.

", "votes": 0, "replies": [] }, { "id": 1028447, "author_name": "quadcore/Richard Epstein", "author_url": "", "post_date": "2020-09-26T21:18:53.277000", "content": "

In a Notebook, I failed with Simple ITK on any image in this competition.

\n

But Simple ITK could read images from another competition (Pulmonary Fibrosis). So Simple ITK works, but something about the dataset for this competition is causing it problems.

\n

I'm working with Pydicom, and with the GDCM fix, it seems to read everything fine. I know Simple ITK adds some other functionality.

\n

Good luck,

\n

-Rich

", "votes": 0, "replies": [] }, { "id": 1028449, "author_name": "Catadanna", "author_url": "", "post_date": "2020-09-26T21:23:56.607000", "content": "

Hallo, thank you for your answer. I know it works in the notebook in the Pulmonary Fibrosis competition, I used it there. There must be a problem with this other competition.

\n

Good luck to you too and thank you again!

", "votes": 0, "replies": [] }, { "id": 1028686, "author_name": "Marco Stefani", "author_url": "", "post_date": "2020-09-27T05:41:54.697000", "content": "

hi @richardepstein, can you explain me the gdcm fix? I'm stuck with that error and I noticed that is not just the train set but also the private test set to have images not readable.
\nSorry, I'm new to machine learning

", "votes": 0, "replies": [] }, { "id": 1028787, "author_name": "Catadanna", "author_url": "", "post_date": "2020-09-27T07:55:49.663000", "content": "

@neuronffh : Just add to your code :

\n
!conda install -c conda-forge gdcm -y\n
\n

Be aware, you need to turn the Internet \"On\" for that.

", "votes": 0, "replies": [] }, { "id": 1028910, "author_name": "Marco Stefani", "author_url": "", "post_date": "2020-09-27T10:09:54.830000", "content": "

Thank you for the answer!

", "votes": 0, "replies": [] }, { "id": 1028955, "author_name": "quadcore/Richard Epstein", "author_url": "", "post_date": "2020-09-27T10:53:57", "content": "

https://www.kaggle.com/richardepstein/load-gdcm-in-notebook-without-internet

\n

This notebook let's you load gdcm without internet.

", "votes": 2, "replies": [] }, { "id": 1029024, "author_name": "Marco Stefani", "author_url": "", "post_date": "2020-09-27T12:09:01.637000", "content": "

Thank you! It works now

", "votes": 0, "replies": [] } ] } ] }, { "id": 1026976, "author_name": "Marco Stefani", "author_url": "", "post_date": "2020-09-25T17:50:37.923000", "content": "

I had problems reading some of the .dcm in the train set using pydicom. It gave me
\nRuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM)
\nDon't know if it's related

", "votes": 0, "replies": [ { "id": 1026988, "author_name": "Catadanna", "author_url": "", "post_date": "2020-09-25T18:05:01.677000", "content": "

No, I meant the use of Simple ITK library, precisely, not Pydicom.

", "votes": 0, "replies": [] } ] } ], "raw_markdown_by_id": { "1026573": "Did someone have problems reading images with Simple ITK ? \n\nI get this error : \n\n> RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:107:\nsitk::ERROR: Unable to determine ImageIO reader for \"/kaggle/input/rsna-str-pulmonary-embolism-detection/train/b35a5a9787a6/e6e025707e2f/1b058f972dec.dcm\"\n\nI even asked directly on Github but they say it works, it might come from some restrictions in Kaggle. \n\nAny help will be appreciated.\n", "1027952": "Good job, continue like this ! BRAVO ", "1028030": "That file you listed is not one of the files that pydicom needs GDCM for. So that is probably unrelated.\n\nIs that the only file you have trouble with, or are you getting errors on all your files?", "1026976": "I had problems reading some of the .dcm in the train set using pydicom. It gave me\nRuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM)\nDon't know if it's related" } }