diff --git a/xcp_d/data/io_spec.yaml b/xcp_d/data/io_spec.yaml
index 8fbedd9de..63feb0917 100644
--- a/xcp_d/data/io_spec.yaml
+++ b/xcp_d/data/io_spec.yaml
@@ -11,7 +11,10 @@ queries:
             datatype: anat
             desc: null
             extension: .nii.gz
-            space: null
+            space:
+            - T1w
+            - T2w
+            - null
             suffix: dseg
         # transform from native anatomical (T1w or T2w) space to same standard space as BOLD
         # "to" entity will be set later
@@ -33,7 +36,9 @@ queries:
             datatype: anat
             desc: preproc
             extension: .nii.gz
-            space: null
+            space:
+            - null
+            - T2w
             suffix: T1w
         # native T2w-space or T1w-space, preprocessed T2w file
         t2w:
diff --git a/xcp_d/utils/bids.py b/xcp_d/utils/bids.py
index f89136af8..2a737b491 100644
--- a/xcp_d/utils/bids.py
+++ b/xcp_d/utils/bids.py
@@ -268,6 +268,33 @@ def collect_data(
     t2w_files = layout.get(return_type="file", subject=participant_label, **queries["t2w"])
     if not t1w_files and not t2w_files:
         raise FileNotFoundError("No T1w or T2w files found.")
+    elif t1w_files and t2w_files:
+        LOGGER.warning("Both T1w and T1w found. Checking for T1w-space T2w.")
+        temp_query = queries["t2w"].copy()
+        temp_query["space"] = "T1w"
+        temp_t2w_files = layout.get(return_type="file", subject=participant_label, **temp_query)
+        if not temp_t2w_files:
+            LOGGER.warning("No T1w-space T2w found. Checking for T2w-space T1w.")
+            temp_query = queries["t1w"].copy()
+            temp_query["space"] = "T2w"
+            temp_t1w_files = layout.get(
+                return_type="file",
+                subject=participant_label,
+                **temp_query,
+            )
+            queries["t1w"]["space"] = "T2w"
+            if not temp_t1w_files:
+                LOGGER.warning("No T2w-space T1w found. Enabling T2w-only processing.")
+                queries["template_to_anat_xfm"]["to"] = "T2w"
+                queries["anat_to_template_xfm"]["from"] = "T2w"
+                # Nibabies may include space-T2w for some derivatives
+                queries["anat_dseg"]["space"] = ["T2w", None]
+            else:
+                LOGGER.warning("T2w-space T1w found. Processing anatomical images in T2w space.")
+        else:
+            LOGGER.warning("T1w-space T2w found. Processing anatomical images in T1w space.")
+            queries["t2w"]["space"] = "T1w"
+            queries["t1w"]["space"] = ["T1w", None]
     elif t2w_files and not t1w_files:
         LOGGER.warning("T2w found, but no T1w. Enabling T2w-only processing.")
         queries["template_to_anat_xfm"]["to"] = "T2w"