mmiv-ml / fastmonai Goto Github PK
View Code? Open in Web Editor NEWSimplifying deep learning for medical imaging
Home Page: https://fastmonai.no
License: Apache License 2.0
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arvidl ashe3z soulsteel c00cjz00 keyurradia gchetty dancebean softwareimpacts juampatronics ailabteam elsadeghnezhad zekiguvenfastmonai's Issues
Error running the notebook / paper
Hi,
I've got an error running the notebook of the paper (https://colab.research.google.com/github/MMIV-ML/fastMONAI/blob/master/paper/paper.ipynb).
File ["<ipython-input-59-e08cef295d53>"](https://localhost:8080/#), line 2
store_variables(pkl_fn='models/vars.pkl', size, reorder, resample)
^
SyntaxError: positional argument follows keyword argumentI think the line should be
store_variables('models/vars.pkl', size, reorder, resample)(I'm reviewing at openjournals/joss-reviews#5297)
Documentation Site Failed To Build
Hi fastMONAI team, just want to let you know that now fastmonai.no returns 404 on access.
Incompatible with PyTorch CUDA 12
I'm trying to use fastMONAI with some H100 GPUs on an HPC. I've installed PyTorch following their instructions and am using CUDA v12. However, after installing fastMONAI via pip, it seems to revert the PyTorch CUDA version to 11.7.
med_img_reader not finding DICOM in sub-directories
I am using a directory path that contains sub-directories with DICOM files. An error message is produced that no DICOM files could be found. Please add capabilities to find all DICOM files in all sub-directories.
Regression tutorial Missing
The regression tutorial link does not work. Is it available for sharing?
Multimodal medical images as x input?
Thanks for the hard work putting this together! It has been really useful for me.
Is it possible to provide a tuple of images to a datablock as the x value?
I have:
dblock = MedDataBlock(
blocks=(ImageTupleBlock(cls=MedImage), MedMaskBlock),
splitter=RandomSplitter(),
get_x=ColReader('qsm_files'),
get_y=ColReader('seg_files'),
item_tfms=[
PadOrCrop([80, 80, 80]),
RandomFlip(axes=("LR",)),
RandomFlip(axes=("AP",)),
RandomAffine(degrees=(90, 90, 90)),
ZNormalization(),
],
reorder=requires_resampling,
resample=suggested_voxelsize
)
But instead of using get_x=ColReader('qsm_files'), I want to retrieve multiple medical images to learn from multimodal data. I do not see any example of this and am unsure how to approach it. Do you have any advice?
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