Hello,
\nI am getting the following error when I try to access the pixel array of DICOM: RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM)
\nSomeone can help ?
\nThanks
Hello,
\nI am getting the following error when I try to access the pixel array of DICOM: RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM)
\nSomeone can help ?
\nThanks
From my experience, what is found is that previously I used to do the code like
\n**Old Method😓😓:
\nimport pydicom as dcm\n\nscan = dcm.dcmread(filepath)\nimg = scan.pixel_array\nwhich oftentimes caused that error. Later I modified the code in the following way:
\n**New Method🤓🤓:
\nimport pydicom\n\nscan = pycdicom.read_file(filepath)\nimg = scan.pixel_array\nThe old method was not that reliable. It sometimes ran properly sometimes not. But the new method never failed me…
", "rawMarkdown": "From my experience, what is found is that previously I used to do the code like \n\n**Old Method😓😓: \n```\nimport pydicom as dcm\n\nscan = dcm.dcmread(filepath)\nimg = scan.pixel_array\n```\nwhich oftentimes caused that error. Later I modified the code in the following way:\n\n**New Method🤓🤓: \n```\nimport pydicom\n\nscan = pycdicom.read_file(filepath)\nimg = scan.pixel_array\n```\n\nThe old method was not that reliable. It sometimes ran properly sometimes not. But the new method never failed me... ", "votes": 2 }, { "id": 1007636, "postDate": "2020-09-12T10:53:28.493Z", "content": "Unfortunately, if you're training on windows, even the conda version of gdcm does not work with python 3.7 or 3.8, so you'll need a python 3.6 environment if you want to use conda install -c conda-forge gdcm
I had the same problem previously and raised a topic for it. And my solution was the same conda line to install. However, I decided to switch to vtk which was featured here. I found this on the other similar competition that had files in DICOM too.
As far as I tested, vtk has yet to raise a single exception when handling DICOM files.
If you want to see how to use it, go to my notebook here.
\nHope this helps.
", "rawMarkdown": "I had the same problem previously and raised a [topic](https://www.kaggle.com/c/rsna-str-pulmonary-embolism-detection/discussion/182144) for it. And my solution was the same `conda` line to install. However, I decided to switch to `vtk` which was featured [here](https://www.kaggle.com/eladwar/20-seconds-or-less). I found this on the other similar [competition](https://www.kaggle.com/c/osic-pulmonary-fibrosis-progression/discussion) that had files in DICOM too.\n\nAs far as I tested, `vtk` has yet to raise a single exception when handling DICOM files.\n\nIf you want to see how to use it, go to my notebook [here](https://www.kaggle.com/seraphwedd18/pe-detection-with-keras-model-creation#Check-Targets-and-Input-Image).\n\nHope this helps." }, { "id": 1009424, "postDate": "2020-09-14T02:17:28.943Z", "content": "None of the proposed fixes have solved the problem for me in Kaggle Notebooks, though it only occurred in 2/12 cases for me (see here). I've yet to try it on another platform.
", "rawMarkdown": "None of the proposed fixes have solved the problem for me in Kaggle Notebooks, though it only occurred in 2/12 cases for me (see [here](https://www.kaggle.com/wfwiggins203/exploring-the-dicom-metadata-images-with-fast-ai)). I've yet to try it on another platform." }, { "id": 1006815, "postDate": "2020-09-11T15:11:46.580Z", "content": "I had the same error, running it multiple times will solve the issue
", "rawMarkdown": "I had the same error, running it multiple times will solve the issue", "replies": [ { "id": 1006926, "postDate": "2020-09-11T16:44:58.473Z", "content": "Hello Alaa,
\nI solved the problem ! The solution is to put !conda install -c conda-forge gdcm -y at the beginning of your notebook.
\nGood luck
That was helpful, thank you!
", "rawMarkdown": "That was helpful, thank you!", "votes": 1 }, { "id": 1009353, "postDate": "2020-09-13T22:26:48.483Z", "content": "how will it install during inference if there is no internet? you might have to add it as external data?
", "rawMarkdown": "how will it install during inference if there is no internet? you might have to add it as external data?" } ] } ], "comments": [ { "id": 1009125, "author_name": "Redwan Sony", "author_url": "", "post_date": "2020-09-13T17:06:10.560000", "content": "From my experience, what is found is that previously I used to do the code like
\n**Old Method😓😓:
\nimport pydicom as dcm\n\nscan = dcm.dcmread(filepath)\nimg = scan.pixel_array\nwhich oftentimes caused that error. Later I modified the code in the following way:
\n**New Method🤓🤓:
\nimport pydicom\n\nscan = pycdicom.read_file(filepath)\nimg = scan.pixel_array\nThe old method was not that reliable. It sometimes ran properly sometimes not. But the new method never failed me…
", "votes": 2, "replies": [] }, { "id": 1007636, "author_name": "James Howard", "author_url": "", "post_date": "2020-09-12T10:53:28.493000", "content": "Unfortunately, if you're training on windows, even the conda version of gdcm does not work with python 3.7 or 3.8, so you'll need a python 3.6 environment if you want to use conda install -c conda-forge gdcm
I had the same problem previously and raised a topic for it. And my solution was the same conda line to install. However, I decided to switch to vtk which was featured here. I found this on the other similar competition that had files in DICOM too.
As far as I tested, vtk has yet to raise a single exception when handling DICOM files.
If you want to see how to use it, go to my notebook here.
\nHope this helps.
", "votes": 0, "replies": [] }, { "id": 1009424, "author_name": "Walter Wiggins", "author_url": "", "post_date": "2020-09-14T02:17:28.943000", "content": "None of the proposed fixes have solved the problem for me in Kaggle Notebooks, though it only occurred in 2/12 cases for me (see here). I've yet to try it on another platform.
", "votes": 0, "replies": [] }, { "id": 1006815, "author_name": "Alaa Triki", "author_url": "", "post_date": "2020-09-11T15:11:46.580000", "content": "I had the same error, running it multiple times will solve the issue
", "votes": 0, "replies": [ { "id": 1006926, "author_name": "TOUCAN", "author_url": "", "post_date": "2020-09-11T16:44:58.473000", "content": "Hello Alaa,
\nI solved the problem ! The solution is to put !conda install -c conda-forge gdcm -y at the beginning of your notebook.
\nGood luck
That was helpful, thank you!
", "votes": 1, "replies": [] }, { "id": 1009353, "author_name": "hirviö", "author_url": "", "post_date": "2020-09-13T22:26:48.483000", "content": "how will it install during inference if there is no internet? you might have to add it as external data?
", "votes": 0, "replies": [] } ] } ], "raw_markdown_by_id": { "1006769": "Hello, \n\nI am getting the following error when I try to access the pixel array of DICOM: RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM)\nSomeone can help ?\nThanks", "1009125": "From my experience, what is found is that previously I used to do the code like \n\n**Old Method😓😓: \n```\nimport pydicom as dcm\n\nscan = dcm.dcmread(filepath)\nimg = scan.pixel_array\n```\nwhich oftentimes caused that error. Later I modified the code in the following way:\n\n**New Method🤓🤓: \n```\nimport pydicom\n\nscan = pycdicom.read_file(filepath)\nimg = scan.pixel_array\n```\n\nThe old method was not that reliable. It sometimes ran properly sometimes not. But the new method never failed me... ", "1007636": "Unfortunately, if you're training on windows, even the `conda` version of `gdcm` does not work with python 3.7 or 3.8, so you'll need a python 3.6 environment if you want to use `conda install -c conda-forge gdcm`", "1009614": "I had the same problem previously and raised a [topic](https://www.kaggle.com/c/rsna-str-pulmonary-embolism-detection/discussion/182144) for it. And my solution was the same `conda` line to install. However, I decided to switch to `vtk` which was featured [here](https://www.kaggle.com/eladwar/20-seconds-or-less). I found this on the other similar [competition](https://www.kaggle.com/c/osic-pulmonary-fibrosis-progression/discussion) that had files in DICOM too.\n\nAs far as I tested, `vtk` has yet to raise a single exception when handling DICOM files.\n\nIf you want to see how to use it, go to my notebook [here](https://www.kaggle.com/seraphwedd18/pe-detection-with-keras-model-creation#Check-Targets-and-Input-Image).\n\nHope this helps.", "1009424": "None of the proposed fixes have solved the problem for me in Kaggle Notebooks, though it only occurred in 2/12 cases for me (see [here](https://www.kaggle.com/wfwiggins203/exploring-the-dicom-metadata-images-with-fast-ai)). I've yet to try it on another platform.", "1006815": "I had the same error, running it multiple times will solve the issue" } }