Comments (7)
Thank you so much for this code, it worked really well. I am impressed with the quality!
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Hi @Meddebma,
Did you get the code running on google colab? I haven't tried this so curious if it worked for you. Thank you!
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Also, we have a function that supports nifti inputs here https://github.com/StanfordMIMI/Comp2Comp/blob/master/comp2comp/io/io_utils.py#L31 but have not yet tested this extensively as a part of the pipelines. We will at this to our todos. We do not currently support nifti outputs, besides the segmentation files which are stored as niftis.
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Hi @louisblankemeier ,
yes it worked perfectly, here is the code:
!git clone https://github.com/StanfordMIMI/Comp2Comp/ %cd Comp2Comp !pip install -e . !bin/C2C spine_muscle_adipose_tissue --input_path /content/drive/MyDrive/CT_body_comp_AI/example/sr
It took 90-120sec per CT scan.
I am really impressed how good it is!
Definitely gonna use it for my next research
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I'm glad it worked for you on colab, that's really good to know!!
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Maybe a Colab version is something we post on the repo as an example use case? Perhaps with voxel integration for viewing?
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Agreed!! I think we've surfaced several cases where people would want to interact with outputs in python (going beyond the CL interface) and a colab tutorial would be well suited here. As you mentioned, one case is visualizing outputs for development and QA, and voxel would be perfect for that! I think we should add this to the top of our TODOs.
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Related Issues (20)
- dicom_to_nifti orientation issue
- way to distinguish multiple series in the same folder
- Cannot slice image objects; consider using img.slicer[slice] to generate a sliced image (see documentation for caveats) or slicing image array data with img.dataobj[slice] or img.get_fdata()[slice] HOT 2
- Why does the latest version not support 2D image segmentation and segmentation result output?
- Local Implementation @ AppleSilicon M1 HOT 6
- load model correction, SpineComputeROIs inconsistent error HOT 10
- Todos
- Error handling in C2C argument HOT 1
- ImportError: libXrender.so
- Per-pipeline installation HOT 1
- Tensorflow version
- Nested pipelines HOT 9
- Add XGBoost dependency for phase_contrast pipeline
- Master pipeline HOT 1
- Add a ToCanonical module to liver_spleen_pancreas
- Dicom outputs
- Manual adjustment of segmentation output HOT 10
- Update Contrast Phase Pipeline with DicomToNifti Module
- get_dicom_or_nifti_paths_and_num naming HOT 4
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