apply_brain_mask.py

[clpalomi]

Hi all,

I am running TractSeg preprocessing pipeline on Linux provided at the page, which includes the following step:

python ~/dev/bsp/scripts/misc/apply_brain_mask.py Diffusion_denoise_unr_eddy_bias.nii.gz \
    Diffusion_denoise_unr_eddy_bias_brain.nii.gz nodif_brain_mask.nii.gz
    cp -v Diffusion_denoise_unr_eddy_bias.bvals Diffusion_denoise_unr_eddy_bias_brain.bvals
    cp -v Diffusion_denoise_unr_eddy_bias.bvecs Diffusion_denoise_unr_eddy_bias_brain.bvecs
}

Here I get an error, as ~/dev/bsp/scripts/misc/apply_brain_mask.py cannot be found. How do I fix this?

Thank you for your help, Claudio

[wasserth]

Thanks for this hint. This is indeed missing. I added it to tractseg/resources/utility_scripts/apply_brain_mask.py and adapted the path in the preprocessing pipeline. Now it should work.