diff --git a/docs/README.md b/docs/README.md index 1d33f6f..0a7dbdb 100644 --- a/docs/README.md +++ b/docs/README.md @@ -185,7 +185,10 @@ sourcing the entire FSL environment. Instead, you should just put `slicesdir` in In additon, you should set: -> export FSLOUTPUTTYPE=NIFTI_GZ +``` +export FSLDIR=/path/to/fsl-6.0.7/ +export FSLOUTPUTTYPE=NIFTI_GZ +``` # Singularity container diff --git a/tests/README.md b/tests/README.md index 8697d6b..d1c2b87 100644 --- a/tests/README.md +++ b/tests/README.md @@ -7,6 +7,7 @@ it is depdendent on the following executables: * dcm2niix * fslroi * bet +* antsRegistrationSyNQuick.sh We recommend only putting the above executables in `PATH` without sourcing extenal environments such as FSL's. For example--`fslroi`, `bet` could be put in `PATH` as: @@ -15,7 +16,10 @@ such as FSL's. For example--`fslroi`, `bet` could be put in `PATH` as: In addition, you need to set: -> export FSLOUTPUTTYPE=NIFTI_GZ +``` +export FSLDIR=/path/to/fsl-6.0.7/ +export FSLOUTPUTTYPE=NIFTI_GZ +``` Moreover, you can put an `exit` statement after any line between 70-81 to run one or more tests: https://github.com/pnlbwh/CNN-Diffusion-MRIBrain-Segmentation/blob/a81ef7e939714f88b67c0a6e84a0ff6db7004622/tests/pipeline_test.sh#L70-L81