diff --git a/.ci/test_template.sh b/.ci/test_template.sh
index 4512e33c6752be17f3cabdd4351407b7ab30cba7..711a66604f20cd9b4d9bd5546efeedfb5b93cd39 100644
--- a/.ci/test_template.sh
+++ b/.ci/test_template.sh
@@ -24,9 +24,9 @@ TEST_OPTS="--cov-report= --cov-append"
 # We run some tests under xvfb-run
 # because they invoke wx. Sleep in
 # between, otherwise xvfb gets upset.
-xvfb-run -a pytest $TEST_OPTS tests/test_idle.py
+xvfb-run -a pytest $TEST_OPTS fsl/tests/test_idle.py
 sleep 5
-xvfb-run -a pytest $TEST_OPTS tests/test_platform.py
+xvfb-run -a pytest $TEST_OPTS fsl/tests/test_platform.py
 
 # We run the immv/imcp tests as the nobody
 # user because some tests expect permission
@@ -36,11 +36,15 @@ xvfb-run -a pytest $TEST_OPTS tests/test_platform.py
 # unintuitively, includes nobody)
 chmod -R a+w `pwd`
 cmd="source /test.venv/bin/activate && pytest"
-cmd="$cmd $TEST_OPTS tests/test_scripts/test_immv_imcp.py tests/test_immv_imcp.py"
+cmd="$cmd $TEST_OPTS fsl/tests/test_scripts/test_immv_imcp.py fsl/tests/test_immv_imcp.py"
 su -s /bin/bash -c "$cmd" nobody
 
 # All other tests can be run as normal.
-pytest $TEST_OPTS -m 'not longtest' --ignore=tests/test_idle.py --ignore=tests/test_platform.py --ignore=tests/test_immv_imcp.py --ignore=tests/test_scripts/test_immv_imcp.py
+pytest $TEST_OPTS -m 'not longtest'         \
+       --ignore=fsl/tests/test_idle.py      \
+       --ignore=fsl/tests/test_platform.py  \
+       --ignore=fsl/tests/test_immv_imcp.py \
+       --ignore=fsl/tests/test_scripts/test_immv_imcp.py
 
 # Long tests are only run on release branches
 if [[ $CI_COMMIT_REF_NAME == v* ]]; then