Skip to content

[FIX] Improve determination of ANTSPATH in BrainExtraction interface #2294

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Nov 22, 2017
Merged

[FIX] Improve determination of ANTSPATH in BrainExtraction interface #2294

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 15 additions & 13 deletions nipype/interfaces/ants/segmentation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -720,17 +720,19 @@ class BrainExtraction(ANTSCommand):
def _run_interface(self, runtime, correct_return_codes=(0,)):
# antsBrainExtraction.sh requires ANTSPATH to be defined
out_environ = self._get_environ()
if out_environ.get('ANTSPATH') is None:
runtime.environ.update(out_environ)
executable_name = self.cmd.split()[0]
exist_val, cmd_path = _exists_in_path(executable_name, runtime.environ)
if not exist_val:
raise IOError("command '%s' could not be found on host %s" %
(self.cmd.split()[0], runtime.hostname))

# Set the environment variable if found
runtime.environ.update({'ANTSPATH': os.path.dirname(cmd_path)})

ants_path = out_environ.get('ANTSPATH', None) or os.getenv('ANTSPATH', None)
if ants_path is None:
# Check for antsRegistration, which is under bin/ (the $ANTSPATH) instead of
# checking for antsBrainExtraction.sh which is under script/
_, cmd_path = _exists_in_path('antsRegistration', runtime.environ)
if not cmd_path:
raise RuntimeError(
'The environment variable $ANTSPATH is not defined in host "%s", '
'and Nipype could not determine it automatically.' % runtime.hostname)
ants_path = os.path.dirname(cmd_path)

self.inputs.environ.update({'ANTSPATH': ants_path})
runtime.environ.update({'ANTSPATH': ants_path})
runtime = super(BrainExtraction, self)._run_interface(runtime)

# Still, double-check if it didn't found N4
Expand All @@ -740,8 +742,8 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
tool = line.strip().replace('we cant find the', '').split(' ')[0]
break

errmsg = ('antsBrainExtraction.sh requires %s the environment variable '
'ANTSPATH to be defined' % tool)
errmsg = ('antsBrainExtraction.sh requires "%s" to be found in $ANTSPATH '
'($ANTSPATH="%s").') % (tool, ants_path)
if runtime.stderr is None:
runtime.stderr = errmsg
else:
Expand Down