diff --git a/pyproject.toml b/pyproject.toml
index a5c5a2ab289..578e9e81e34 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -90,6 +90,9 @@ cmd = '''cmake \
   -DModule_TextureFeatures:BOOL=ON \
   -DModule_Thickness3D:BOOL=ON \
   -DModule_VariationalRegistration:BOOL=ON \
+  -DITK_USE_FFTWF:BOOL=ON \
+  -DITK_USE_FFTWD:BOOL=OFF \
+  -DITK_USE_SYSTEM_FFTW:BOOL=OFF \
   -DITK_COMPUTER_MEMORY_SIZE:STRING=5'''
 description = "Configure ITK for CI (with ccache compiler launcher)"
 outputs = ["build/CMakeFiles/"]