[BUG] antsBrainExtraction interface fails when $ANTSPATH is not defined, but exit code is 0

[oesteban]

Summary

antsBrainExtraction interface fails when $ANTSPATH is not defined, but exit code is 0

How to replicate the behavior

The problem is the following

$ antsBrainExtraction.sh -h
we cant find the N4 program -- does not seem to exist. please (re)define $ANTSPATH in your environment.
$ echo $?
0

when nipype gets to check the output, since the exit code is zero, it breaks. We could check, at least, for this output message and reraise the message.

cc @rwblair .

[chrisgorgo]

is this stdout or stderr?

…

On Tue, Mar 21, 2017 at 4:56 PM, Oscar Esteban ***@***.***> wrote: Summary antsBrainExtraction interface fails when $ANTSPATH is not defined, but exit code is 0 How to replicate the behavior The problem is the following $ antsBrainExtraction.sh -h we cant find the N4 program -- does not seem to exist. please (re)define $ANTSPATH in your environment. $ echo $? 0 when nipype gets to check the output, since the exit code is zero, it breaks. We could check, at least, for this output message and reraise the message. cc @rwblair <https://github.com/rwblair> . — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1901>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkp3svhDYl8vw07ed4tJoMm-lDyYaJks5roGOngaJpZM4Mkjxu> .

[oesteban]

stdout:

$ antsBrainExtraction.sh > out 2> error
$ cat error 
$ cat out 
we cant find the N4 program -- does not seem to exist. please (re)define $ANTSPATH in your environment.