From 5d6b83d5a838bb55af267eb33833cf20f692aa4e Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 23 Jun 2023 13:22:11 +0200
Subject: [PATCH 1/3] fix: enable stdout and stderr capture for fALFF via AFNI

---
 junifer/markers/falff/falff_estimator.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/junifer/markers/falff/falff_estimator.py b/junifer/markers/falff/falff_estimator.py
index 035a9eaca..f6bf57cae 100644
--- a/junifer/markers/falff/falff_estimator.py
+++ b/junifer/markers/falff/falff_estimator.py
@@ -70,12 +70,11 @@ class ALFFEstimator:
             If AFNI command fails.
         """
         logger.info(f"AFNI command to be executed: {cmd}")
-        # TODO: Figure out how to capture stdout and stderr
         process = subprocess.run(
             cmd,
             stdin=subprocess.DEVNULL,
-            # stdout=subprocess.STDOUT,
-            # stderr=subprocess.STDOUT,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
             shell=True,
             check=False,
         )
-- 
2.52.0


From 63d5a3c8c654da7b62ad077c0507348530d6aa84 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 23 Jun 2023 13:22:53 +0200
Subject: [PATCH 2/3] fix: enable stdout and stderr capture for ReHo via AFNI

---
 junifer/markers/reho/reho_estimator.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/junifer/markers/reho/reho_estimator.py b/junifer/markers/reho/reho_estimator.py
index 8d3d2802f..211c5d44c 100644
--- a/junifer/markers/reho/reho_estimator.py
+++ b/junifer/markers/reho/reho_estimator.py
@@ -173,6 +173,8 @@ class ReHoEstimator:
         reho_process = subprocess.run(
             reho_cmd_str,  # string needed with shell=True
             stdin=subprocess.DEVNULL,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
             shell=True,  # needed for respecting $PATH
             check=False,
         )
@@ -205,6 +207,8 @@ class ReHoEstimator:
         convert_process = subprocess.run(
             convert_cmd_str,  # string needed with shell=True
             stdin=subprocess.DEVNULL,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
             shell=True,  # needed for respecting $PATH
             check=False,
         )
-- 
2.52.0


From ef5f43d22245000935b371042d1a356ee8d1d30d Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 26 Jun 2023 09:04:48 +0200
Subject: [PATCH 3/3] chore: add changelog 234.enh

---
 docs/changes/newsfragments/234.enh | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 docs/changes/newsfragments/234.enh

diff --git a/docs/changes/newsfragments/234.enh b/docs/changes/newsfragments/234.enh
new file mode 100644
index 000000000..60eddbb85
--- /dev/null
+++ b/docs/changes/newsfragments/234.enh
@@ -0,0 +1 @@
+Enable ``stdout`` and ``stderr`` capture for AFNI commands by `Synchon Mandal`_
-- 
2.52.0