I get the following error when trying to view some DICOMs:
\nRuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. ), pylibjpeg (req. )\nDoes anybody know how to resolve this issue? I tried to pip install gdcm but that didn't solve it…
I get the following error when trying to view some DICOMs:
\nRuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. ), pylibjpeg (req. )\nDoes anybody know how to resolve this issue? I tried to pip install gdcm but that didn't solve it…
I solved the error by running this script at the beginning of the code.
\nI am referring to SIIM-COVID19: Classification Only PyTorch Starter.
! conda install -c conda-forge gdcm -y\nTry it!!!
", "rawMarkdown": "\n\n\nI solved the error by running this script at the beginning of the code.\n\n\nI am referring to [SIIM-COVID19: Classification Only PyTorch Starter](https://www.kaggle.com/heyytanay/siim-covid19-classification-only-pytorch-starter).\n\n```python\n! conda install -c conda-forge gdcm -y\n```\n\nTry it!!!", "votes": 7, "replies": [ { "id": 1313302, "postDate": "2021-05-18T13:55:50.533Z", "content": "This works, thank you!
", "rawMarkdown": "This works, thank you!" }, { "id": 1314060, "postDate": "2021-05-18T23:25:50.490Z", "content": "Awesome. Thanks!
", "rawMarkdown": "Awesome. Thanks!" }, { "id": 1314232, "postDate": "2021-05-19T03:49:20.447Z", "content": "But code competition does not allow internet access. Is there any easy way?
", "rawMarkdown": "But code competition does not allow internet access. Is there any easy way? ", "votes": 1 }, { "id": 1314286, "postDate": "2021-05-19T04:55:56.467Z", "content": "Hum…
\nHow about a source build from this repository?
\nhttps://sourceforge.net/p/gdcm/gdcm/ci/master/tree/
\nI'm out right now, so I'll try it later.
", "rawMarkdown": "Hum...\n\nHow about a source build from this repository?\n\nhttps://sourceforge.net/p/gdcm/gdcm/ci/master/tree/\n\nI'm out right now, so I'll try it later." }, { "id": 1314295, "postDate": "2021-05-19T05:05:52.580Z", "content": "I found this, so I decided to use it
\nhttps://www.kaggle.com/c/siim-covid19-detection/discussion/239918
", "rawMarkdown": "I found this, so I decided to use it \n\nhttps://www.kaggle.com/c/siim-covid19-detection/discussion/239918" }, { "id": 1314495, "postDate": "2021-05-19T07:35:15.440Z", "content": "That's the best solution!!!!!
", "rawMarkdown": "That's the best solution!!!!!" }, { "id": 1315457, "postDate": "2021-05-19T19:55:47.890Z", "content": "For those looking for gdcm without internet access, check out this notebook
\nhttps://www.kaggle.com/awsaf49/pydicom-conda-helper
I met an error when installing gdcm as following, which means gdcm can't support python 3.7?
\nSpecifications:
\ngdcm -> python[version='2.7.|3.5.|3.6.|3.4.']
\nYour python: python=3.7
If python is on the left-most side of the chain, that's the version you've asked for.
\nWhen python appears to the right, that indicates that the thing on the left is somehow
\nnot available for the python version you are constrained to. Note that conda will not
\nchange your python version to a different minor version unless you explicitly specify
\nthat.
Note that strict channel priority may have removed packages required for satisfiability.
", "rawMarkdown": "I met an error when installing gdcm as following, which means gdcm can't support python 3.7?\n\n*****************************************************************************************\nSpecifications:\n\ngdcm -> python[version='2.7.|3.5.|3.6.|3.4.']\nYour python: python=3.7\n\nIf python is on the left-most side of the chain, that's the version you've asked for.\nWhen python appears to the right, that indicates that the thing on the left is somehow\nnot available for the python version you are constrained to. Note that conda will not\nchange your python version to a different minor version unless you explicitly specify\nthat.\n\nNote that strict channel priority may have removed packages required for satisfiability.\n\n" }, { "id": 1338085, "postDate": "2021-06-06T06:52:58.077Z", "content": "it did not solve problem for me .I even did conda install forge
", "rawMarkdown": "it did not solve problem for me .I even did conda install forge" }, { "id": 1340596, "postDate": "2021-06-08T06:08:40.950Z", "content": "@awsaf49 Nice solution!
", "rawMarkdown": "@awsaf49 Nice solution!" } ] }, { "id": 1357616, "postDate": "2021-06-19T20:26:36.883Z", "content": "I tried the solutions below but I still get errors on Kaggle notebook while trying to visualize images using imshow. Any suggestions?
", "rawMarkdown": "I tried the solutions below but I still get errors on Kaggle notebook while trying to visualize images using imshow. Any suggestions?" }, { "id": 1329782, "postDate": "2021-05-31T11:13:55.310Z", "content": "You can use 'python-gdcm' instead.
\nFor using without the internet:
thanks very much. it's great
", "rawMarkdown": "thanks very much. it's great" } ] }, { "id": 1329291, "postDate": "2021-05-31T03:23:46.103Z", "rawMarkdown": "", "isDeleted": true }, { "id": 1331204, "postDate": "2021-06-01T10:33:07.017Z", "content": "thank you a lot
", "rawMarkdown": "thank you a lot" } ], "comments": [ { "id": 1312873, "author_name": "chizuchizu", "author_url": "", "post_date": "2021-05-18T09:48:26.283000", "content": "I solved the error by running this script at the beginning of the code.
\nI am referring to SIIM-COVID19: Classification Only PyTorch Starter.
! conda install -c conda-forge gdcm -y\nTry it!!!
", "votes": 7, "replies": [ { "id": 1313302, "author_name": "Kerem Turgutlu", "author_url": "", "post_date": "2021-05-18T13:55:50.533000", "content": "This works, thank you!
", "votes": 0, "replies": [] }, { "id": 1314060, "author_name": "Darien Schettler", "author_url": "", "post_date": "2021-05-18T23:25:50.490000", "content": "Awesome. Thanks!
", "votes": 0, "replies": [] }, { "id": 1314232, "author_name": "Tanrei(nama)", "author_url": "", "post_date": "2021-05-19T03:49:20.447000", "content": "But code competition does not allow internet access. Is there any easy way?
", "votes": 1, "replies": [] }, { "id": 1314286, "author_name": "chizuchizu", "author_url": "", "post_date": "2021-05-19T04:55:56.467000", "content": "Hum…
\nHow about a source build from this repository?
\nhttps://sourceforge.net/p/gdcm/gdcm/ci/master/tree/
\nI'm out right now, so I'll try it later.
", "votes": 0, "replies": [] }, { "id": 1314295, "author_name": "Tanrei(nama)", "author_url": "", "post_date": "2021-05-19T05:05:52.580000", "content": "I found this, so I decided to use it
\nhttps://www.kaggle.com/c/siim-covid19-detection/discussion/239918
", "votes": 0, "replies": [] }, { "id": 1314495, "author_name": "chizuchizu", "author_url": "", "post_date": "2021-05-19T07:35:15.440000", "content": "That's the best solution!!!!!
", "votes": 0, "replies": [] }, { "id": 1315457, "author_name": "Awsaf", "author_url": "", "post_date": "2021-05-19T19:55:47.890000", "content": "For those looking for gdcm without internet access, check out this notebook
\nhttps://www.kaggle.com/awsaf49/pydicom-conda-helper
I met an error when installing gdcm as following, which means gdcm can't support python 3.7?
\nSpecifications:
\ngdcm -> python[version='2.7.|3.5.|3.6.|3.4.']
\nYour python: python=3.7
If python is on the left-most side of the chain, that's the version you've asked for.
\nWhen python appears to the right, that indicates that the thing on the left is somehow
\nnot available for the python version you are constrained to. Note that conda will not
\nchange your python version to a different minor version unless you explicitly specify
\nthat.
Note that strict channel priority may have removed packages required for satisfiability.
", "votes": 0, "replies": [] }, { "id": 1338085, "author_name": "Jaideep", "author_url": "", "post_date": "2021-06-06T06:52:58.077000", "content": "it did not solve problem for me .I even did conda install forge
", "votes": 0, "replies": [] }, { "id": 1340596, "author_name": "README", "author_url": "", "post_date": "2021-06-08T06:08:40.950000", "content": "@awsaf49 Nice solution!
", "votes": 0, "replies": [] } ] }, { "id": 1357616, "author_name": "kanishk patel", "author_url": "", "post_date": "2021-06-19T20:26:36.883000", "content": "I tried the solutions below but I still get errors on Kaggle notebook while trying to visualize images using imshow. Any suggestions?
", "votes": 0, "replies": [] }, { "id": 1329782, "author_name": "Vysakh Nair", "author_url": "", "post_date": "2021-05-31T11:13:55.310000", "content": "You can use 'python-gdcm' instead.
\nFor using without the internet:
thanks very much. it's great
", "votes": 0, "replies": [] } ] }, { "id": 1329291, "author_name": "", "author_url": "", "post_date": "2021-05-31T03:23:46.103000", "content": "", "votes": 0, "replies": [] }, { "id": 1331204, "author_name": "tensor choko", "author_url": "", "post_date": "2021-06-01T10:33:07.017000", "content": "thank you a lot
", "votes": 0, "replies": [] } ], "raw_markdown_by_id": { "1312325": "I get the following error when trying to view some DICOMs:\n\n```\nRuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. ), pylibjpeg (req. )\n```\n\nDoes anybody know how to resolve this issue? I tried to `pip install gdcm` but that didn't solve it...", "1312873": "\n\n\nI solved the error by running this script at the beginning of the code.\n\n\nI am referring to [SIIM-COVID19: Classification Only PyTorch Starter](https://www.kaggle.com/heyytanay/siim-covid19-classification-only-pytorch-starter).\n\n```python\n! conda install -c conda-forge gdcm -y\n```\n\nTry it!!!", "1357616": "I tried the solutions below but I still get errors on Kaggle notebook while trying to visualize images using imshow. Any suggestions?", "1329782": "You can use 'python-gdcm' instead.\nFor using without the internet:\n1. Download the 'python_gdcm-3.0.9.0-cp37-cp37m-manylinux2014_x86_64.whl' file using the command '!pip download python-gdcm'.\n2. Upload the downloaded .whl file to the notebook without internet.\n3. Then install using the command '!pip install python_gdcm-3.0.9.0-cp37-cp37m-manylinux2014_x86_64.whl'.\n4. Import gdcm.", "1329291": "", "1331204": "thank you a lot" } }