--- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ - + [](https://doi.org/10.5281/zenodo.3665739) []() []() @@ -121,17 +121,17 @@ You can build ANTs following their [GitHub](https://github.com/ANTsX/ANTs). Or you can use our pre-built ANTs: -> conda install -y pnlbwh::ants +conda install -y pnlbwh::ants Either way, you need to set the environment variable `ANTSPATH`. For the latter method, it is: -> export ANTSPATH=${CONDA_PREFIX}/bin +export ANTSPATH=${CONDA_PREFIX}/bin ## 4. CUDA environment To run this program on GPU, you must set `LD_LIBRARY_PATH`: -> export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib/:${LD_LIBRARY_PATH} +export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib/:${LD_LIBRARY_PATH} Your NVIDIA driver should be compatible with CUDA. @@ -193,7 +193,7 @@ to generate snapshots of image-mask for being able to QC it. Hence, we do not recommend sourcing the entire FSL environment. Instead, you should just put `slicesdir` in your PATH: -> export PATH=/path/to/fsl-6.0.7/share/fsl/bin:$PATH +export PATH=/path/to/fsl-6.0.7/share/fsl/bin:$PATH In additon, you should set: @@ -278,14 +278,14 @@ Whether you register the images or not, create a text file for with their absolute paths: -> b0_list.txt + b0_list.txt /path/to/case1_b0.nii.gz /path/to/case2_b0.nii.gz ... -> mask_list.txt +mask_list.txt /path/to/case1_mask.nii.gz /path/to/case2_mask.nii.gz