From cc5d6ffcd62e7ee23b583356754b396b4b670eb0 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 19 Mar 2020 10:56:14 +0000
Subject: [PATCH] RF: runfsl errors on non-FSL commands
---
fsl/utils/run.py | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index db6af1925..7211965d7 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -3,6 +3,7 @@
# run.py - Functions for running shell commands
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
"""This module provides some functions for running shell commands.
@@ -358,6 +359,12 @@ def runfsl(*args, **kwargs):
args[0] = cmdpath
break
+ # error if the command cannot
+ # be found in a FSL directory
+ else:
+ raise FileNotFoundError('FSL tool {} not found (checked {})'.format(
+ args[0], ', '.join(prefixes)))
+
return run(*args, **kwargs)
--
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