diff --git a/docs/changes/newsfragments/356.bugfix b/docs/changes/newsfragments/356.bugfix
new file mode 100644
index 000000000..2c5c196a8
--- /dev/null
+++ b/docs/changes/newsfragments/356.bugfix
@@ -0,0 +1 @@
+Fix ``mri_binarize`` command preparation for structures with multiple indices in :class:`.BrainPrint` by `Fede Raimondo`_
diff --git a/junifer/markers/brainprint.py b/junifer/markers/brainprint.py
index d5deb7bd4..13c36a1e3 100644
--- a/junifer/markers/brainprint.py
+++ b/junifer/markers/brainprint.py
@@ -143,7 +143,7 @@ class BrainPrint(BaseMarker):
         mri_binarize_cmd = [
             "mri_binarize",
             f"--i {aseg_path.resolve()}",
-            f"--match {''.join(indices)}",
+            f"--match {' '.join(indices)}",
             f"--o {mri_binarize_output_path.resolve()}",
         ]
         # Call mri_binarize command