From 57e1af29573684ea5aaf3b6fd546856688669794 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Fri, 25 Oct 2019 14:35:53 -0400 Subject: [PATCH] doc: update note for singularity environment variables closes #13 --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 9af4cca..831d57f 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,8 @@ singularity run -B $(pwd):/data -W /data --nv kwyk_latest-gpu.sif -m bvwn_multi_ --save-variance --save-entropy T1_001.nii.gz output ``` +Note: If you already have `FREESURFER` environment variables in your shell, these may interfere with the ones inside the container. To isolate the container further please add the `-e` flag at the beginning (`singularity run -e ...`) to suppress any environment variables from being pulled into the container. + This will generate two sets of files `output_*.nii.gz` and `output_*_orig.nii.gz`. The first set consists of results in conformed FreeSurfer space. The second set will correspond to the original input space. 1. `output_means`: This file contains the labels