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MASILab / Synb0-DISCO

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps
https://my.vanderbilt.edu/masi
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python requirements #43

Open rcruces opened 1 year ago

rcruces commented 1 year ago

Could you please provide or point me to the python package versions to build a local environment?

dr-ir-joost commented 10 months ago

Hi,

I created a conda enviroment using the following packages (I have a nvidia GPU with CUDA version 11.8):

conda create -p ~/SynB0-DISCO python=3.6
conda activate ~/SynB0-DISCO
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118 <-- change this line if you have different GPU/CUDA version
pip3 install Pillow six nibabel scipy numpy==1.19

Afterwards, I cloned the Synb0-DISCO repo into the conda enviroment and adapted the /src/pipeline.sh and /data-processing/prepare_input.sh files such that my bin folders of FSL, FreeSurfer, ANTs are found. Note that you will also need the c3d_affine_tool, which is not provided by any of these other tools.