Open Meddebma opened 1 year ago
Thank you so much for this code, it worked really well. I am impressed with the quality!
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!
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.
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
I'm glad it worked for you on colab, that's really good to know!!
Maybe a Colab version is something we post on the repo as an example use case? Perhaps with voxel integration for viewing?
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.
Hi,
is it possible to run comp2comp on google colab? and do you consider to integrate nifti format for input and output images?
Best, Aymen