From 530a97d412f13838c593e4fa782856596172703a Mon Sep 17 00:00:00 2001
From: manuegrx <47973414+manuegrx@users.noreply.github.com>
Date: Thu, 8 Jun 2023 17:26:02 +0200
Subject: [PATCH 1/2] add contrast outputs for EstimatedModel when factor_info
 used in Level1design

---
 nipype/interfaces/spm/model.py                | 51 +++++++++++++++++++
 .../spm/tests/test_auto_EstimateModel.py      |  4 ++
 2 files changed, 55 insertions(+)

diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py
index 8df967573e..498762b04a 100644
--- a/nipype/interfaces/spm/model.py
+++ b/nipype/interfaces/spm/model.py
@@ -245,6 +245,34 @@ class EstimateModelOutputSpec(TraitedSpec):
         ImageFileSPM(exists=True),
         desc="Images of the standard deviation of parameter posteriors",
     )
+    con_images = OutputMultiPath(
+        File(exists=True),
+        desc=(
+            "contrast images from a t-contrast "
+            "(created if factor_info used in Level1Design)"
+        ),
+    )
+    spmT_images = OutputMultiPath(
+        File(exists=True),
+        desc=(
+            "stat images from a t-contrast"
+            "(created if factor_info used in Level1Design)"
+        ),
+    )
+    ess_images = OutputMultiPath(
+        File(exists=True),
+        desc=(
+            "contrast images from an F-contrast"
+            "(created if factor_info used in Level1Design)"
+        ),
+    )
+    spmF_images = OutputMultiPath(
+        File(exists=True),
+        desc=(
+            "stat images from an F-contrast"
+            "(created if factor_info used in Level1Design)"
+        ),
+    )
 
 
 class EstimateModel(SPMCommand):
@@ -310,6 +338,29 @@ def _list_outputs(self):
                 outputs["residual_images"] = glob(os.path.join(pth, "Res_*"))
             if betas:
                 outputs["beta_images"] = [os.path.join(pth, beta) for beta in betas]
+            # When 'factor_info' is used in Level1Design
+            # spm automatically creates contrast
+            try:
+                contrast = [c.Vcon[0][0].fname[0] for c in spm["SPM"][0, 0].xCon[0]]
+                contrast_spm = [c.Vspm[0][0].fname[0] for c in spm["SPM"][0, 0].xCon[0]]
+            except Exception:
+                contrast = []
+                contrast_spm = []
+
+            if contrast:
+                outputs["con_images"] = [
+                    (os.path.join(pth, cont) for cont in contrast if 'con' in cont)
+                ]
+                outputs["ess_images"] = [
+                    (os.path.join(pth, cont) for cont in contrast if 'ess' in cont)
+                ]
+            if contrast_spm:
+                outputs["spmT_images"] = [
+                    (os.path.join(pth, cont) for cont in contrast_spm if 'spmT' in cont)
+                ]
+                outputs["spmF_images"] = [
+                    (os.path.join(pth, cont) for cont in contrast_spm if 'spmF' in cont)
+                ]
 
         outputs["mask_image"] = os.path.join(pth, f"mask.{outtype}")
         outputs["spm_mat_file"] = os.path.join(pth, "SPM.mat")
diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py
index c78924de2f..04c4679767 100644
--- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py
+++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py
@@ -46,6 +46,8 @@ def test_EstimateModel_outputs():
         SDbetas=dict(),
         SDerror=dict(),
         beta_images=dict(),
+        con_images=dict(),
+        ess_images=dict(),
         labels=dict(
             extensions=[".hdr", ".img", ".img.gz", ".nii"],
         ),
@@ -56,6 +58,8 @@ def test_EstimateModel_outputs():
             extensions=[".hdr", ".img", ".img.gz", ".nii"],
         ),
         residual_images=dict(),
+        spmF_images=dict(),
+        spmT_images=dict(),
         spm_mat_file=dict(
             extensions=None,
         ),

From 1467f1c6f874bc5da1d4713df2dfb361a8a4cd2f Mon Sep 17 00:00:00 2001
From: manuegrx <47973414+manuegrx@users.noreply.github.com>
Date: Fri, 9 Jun 2023 11:16:48 +0200
Subject: [PATCH 2/2] fix typo

---
 nipype/interfaces/spm/model.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py
index 498762b04a..89f2be33ea 100644
--- a/nipype/interfaces/spm/model.py
+++ b/nipype/interfaces/spm/model.py
@@ -349,17 +349,17 @@ def _list_outputs(self):
 
             if contrast:
                 outputs["con_images"] = [
-                    (os.path.join(pth, cont) for cont in contrast if 'con' in cont)
+                    os.path.join(pth, cont) for cont in contrast if 'con' in cont
                 ]
                 outputs["ess_images"] = [
-                    (os.path.join(pth, cont) for cont in contrast if 'ess' in cont)
+                    os.path.join(pth, cont) for cont in contrast if 'ess' in cont
                 ]
             if contrast_spm:
                 outputs["spmT_images"] = [
-                    (os.path.join(pth, cont) for cont in contrast_spm if 'spmT' in cont)
+                    os.path.join(pth, cont) for cont in contrast_spm if 'spmT' in cont
                 ]
                 outputs["spmF_images"] = [
-                    (os.path.join(pth, cont) for cont in contrast_spm if 'spmF' in cont)
+                    os.path.join(pth, cont) for cont in contrast_spm if 'spmF' in cont
                 ]
 
         outputs["mask_image"] = os.path.join(pth, f"mask.{outtype}")