From 90f2c941230cfc7d91bfe7194934c35c47f88f49 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Tue, 18 Nov 2025 10:21:03 -0500
Subject: [PATCH 1/2] Collect preprocessed T2w image.

---
 src/smriprep/data/io_spec.json | 10 ++++++++++
 src/smriprep/utils/bids.py     |  5 ++++-
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/smriprep/data/io_spec.json b/src/smriprep/data/io_spec.json
index b3c97c588b..057c8f634f 100644
--- a/src/smriprep/data/io_spec.json
+++ b/src/smriprep/data/io_spec.json
@@ -44,6 +44,16 @@
           ".nii.gz",
           ".nii"
         ]
+      },
+      "t2w_preproc": {
+        "datatype": "anat",
+        "space": null,
+        "desc": "preproc",
+        "suffix": "T2w",
+        "extension": [
+          ".nii.gz",
+          ".nii"
+        ]
       }
     },
     "transforms": {
diff --git a/src/smriprep/utils/bids.py b/src/smriprep/utils/bids.py
index 463391335c..6ac168b476 100644
--- a/src/smriprep/utils/bids.py
+++ b/src/smriprep/utils/bids.py
@@ -70,7 +70,10 @@ def collect_derivatives(
 
         paths = [item.path for item in item]
 
-        derivs_cache[f't1w_{key}'] = paths[0] if len(paths) == 1 else paths
+        if key.startswith('t2w_'):
+            derivs_cache[key] = paths[0] if len(paths) == 1 else paths
+        else:
+            derivs_cache[f't1w_{key}'] = paths[0] if len(paths) == 1 else paths
 
     transforms = derivs_cache.setdefault('transforms', {})
     for _space in std_spaces:

From a103259043876f143883c66bdbc6c4611058d8bd Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo90@gmail.com>
Date: Tue, 18 Nov 2025 10:40:12 -0500
Subject: [PATCH 2/2] Update src/smriprep/utils/bids.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/smriprep/utils/bids.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/smriprep/utils/bids.py b/src/smriprep/utils/bids.py
index 6ac168b476..7d8f9e0786 100644
--- a/src/smriprep/utils/bids.py
+++ b/src/smriprep/utils/bids.py
@@ -70,10 +70,9 @@ def collect_derivatives(
 
         paths = [item.path for item in item]
 
-        if key.startswith('t2w_'):
-            derivs_cache[key] = paths[0] if len(paths) == 1 else paths
-        else:
-            derivs_cache[f't1w_{key}'] = paths[0] if len(paths) == 1 else paths
+        if not key.startswith('t2w_'):
+            key = f't1w_{key}'
+        derivs_cache[key] = paths[0] if len(paths) == 1 else paths
 
     transforms = derivs_cache.setdefault('transforms', {})
     for _space in std_spaces: