diff --git a/.github/workflows/quicktest_runner.yaml b/.github/workflows/quicktest_runner.yaml index 9c42c62c..750e7a08 100644 --- a/.github/workflows/quicktest_runner.yaml +++ b/.github/workflows/quicktest_runner.yaml @@ -128,6 +128,7 @@ jobs: echo "Running FastSurfer..." export FREESURFER_HOME=/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh + export FASTSURFER_HOME=$(pwd) ./brun_fastsurfer.sh --subject_list $RUNNER_FS_MRI_DATA/subjects_list.txt \ --sd $RUNNER_FS_OUTPUT \ --parallel --threads 4 --3T --parallel_subjects surf