# Subprocess.call does not work!
**URL:** https://discourse.slicer.org/t/subprocess-call-does-not-work/2837
**Category:** Support
**Created:** [May 17, 2018, 10:00am UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837 "2018-05-17T10:00:16Z")
**Posts on this page:** 14
**Page:** 1
### Author:  [@wpgao](https://discourse.slicer.org/u/wpgao)
#### Post date: [May 17, 2018, 10:00am UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/1 "2018-05-17T10:00:16Z")
Hi all,
I try to use subprocess.call to run an external application in the python interactor of 3D Slicer but failed! Error message is “terminate called after throwing an instance of ‘H5::DataSpaceIException’”
However, when I run the python in the terminal and input the same command, the application works!
Is there any difference between the two pythons?
Thanks very much!
Operating system: Centos 7
Slicer version: 4.8
Expected behavior:
Actual behavior:
---
### Author:  [@ihnorton](https://discourse.slicer.org/u/ihnorton)
#### Post date: [May 17, 2018, 2:33pm UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/2 "2018-05-17T14:33:05Z")
> [@wpgao](#):
>
> Is there any difference between the two pythons?
Yes, Slicer’s python is [embedded](https://discourse.slicer.org/t/access-slicer-modules-and-libraries-in-pycharm/2765/2).
`subprocess.call` should generally work, however, it will block Slicer (GUI will freeze) until the call completes (you can use `Popen` or Slicer’s CLI infrastructure instead for asynchronous calls). I just tried `subprocess.call(['sleep', '10'])` on linux with a recent nightly, and it worked fine.
Please show a minimal example if you can – maybe someone will notice a problem.
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [May 17, 2018, 4:52pm UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/3 "2018-05-17T16:52:31Z")
The crash is probably because your application tries to use Slicer’s ITK, VTK, HDF5, etc. libraries. If you want to use the default system environment, you can retrieve it using `slicer.util.startupEnvironment()`.
```
from subprocess import check_output
check_output(
["/usr/bin/python3", "-c", "print('hola')"],
env=slicer.util.startupEnvironment())
'hola\n'
```
See details in this post: [Subprocess call in Python interpreter results in memory corruption](https://discourse.slicer.org/t/subprocess-call-in-python-interpreter-results-in-memory-corruption/919/17)
---
### Author:  [@wpgao](https://discourse.slicer.org/u/wpgao)
#### Post date: [May 18, 2018, 10:51am UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/4 "2018-05-18T10:51:54Z")
@ihnorton Thanks for your reply. I just try to call a function of ANTs for image registration!
@lassoan Thanks! It works according to your suggestion. In addition, shell should be set True. Otherwise, it does not work. I don’t know why and there is no any information output to the terminal!
---
### Author:  [@ihnorton](https://discourse.slicer.org/u/ihnorton)
#### Post date: [September 6, 2018, 4:31am UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/5 "2018-09-06T04:31:58Z")
A post was split to a new topic: [Calling C++ from Python](https://discourse.slicer.org/t/calling-c-from-python/3998)
---
### Author:  [@Saima](https://discourse.slicer.org/u/Saima)
#### Post date: [July 8, 2019, 8:53am UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/6 "2019-07-08T08:53:10Z")
Hi andras,
I am extactly doing the same but getting error.
```auto
Traceback (most recent call last):
File "", line 1, in
File "C:\Program Files\Slicer 4.10.2\lib\Python\Lib\subprocess.py", line 212, in check_output
process = Popen(stdout=PIPE, *popenargs, **kwargs)
File "C:\Program Files\Slicer 4.10.2\lib\Python\Lib\subprocess.py", line 390, in __init__
errread, errwrite)
File "C:\Program Files\Slicer 4.10.2\lib\Python\Lib\subprocess.py", line 640, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
```
Would you please suggest what am I doing wrong??
---
### Author:  [@jcfr](https://discourse.slicer.org/u/jcfr)
#### Post date: [July 8, 2019, 1:46pm UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/7 "2019-07-08T13:46:07Z")
The message indicates that the path to the executable is incorrect. So that we can better understand the problem, could you share the code leading to this exception ?
---
### Author:  [@Saima](https://discourse.slicer.org/u/Saima)
#### Post date: [July 9, 2019, 6:56am UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/8 "2019-07-09T06:56:13Z")
I am simply checking it with print statement.
```python
command_line = [r"F:\anaconda3\python3.exe","-c","print('helo')"]
from subprocess import check_output
command_result = check_output(command_line, env = slicer.util.startupEnvironment())
```
---
### Author:  [@Saima](https://discourse.slicer.org/u/Saima)
#### Post date: [July 10, 2019, 7:24am UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/9 "2019-07-10T07:24:44Z")
Hi,
Why am I unable to run the code below
```python
command_line=["F:\anaconda3\python.exe","-c", "print('hola')"]
from subprocess import run
command_result = run(command_line, env =
slicer.util.startupEnvironment())
print(command_result)
```
```auto
Traceback (most recent call last):
File "F:\Slicer 4.11.0-2019-07-06\bin\Python\slicer\ScriptedLoadableModule.py", line 196, in onReload
slicer.util.reloadScriptedModule(self.moduleName)
File "F:\Slicer 4.11.0-2019-07-06\bin\Python\slicer\util.py", line 769, in reloadScriptedModule
moduleName, fp, filePath, ('.py', 'r', imp.PY_SOURCE))
File "F:\Slicer 4.11.0-2019-07-06\lib\Python\Lib\imp.py", line 235, in load_module
return load_source(name, filename, file)
File "F:\Slicer 4.11.0-2019-07-06\lib\Python\Lib\imp.py", line 170, in load_source
module = _exec(spec, sys.modules[name])
File "", line 618, in _exec
File "", line 678, in exec_module
File "", line 219, in _call_with_frames_removed
File "F:/Slicer 4.11.0-2019-07-06/subprocess/subprocess/subprocess.py", line 134, in
slicer.util.startupEnvironment())
File "F:\Slicer 4.11.0-2019-07-06\lib\Python\Lib\subprocess.py", line 403, in run
with Popen(*popenargs, **kwargs) as process:
File "F:\Slicer 4.11.0-2019-07-06\lib\Python\Lib\subprocess.py", line 709, in __init__
restore_signals, start_new_session)
File "F:\Slicer 4.11.0-2019-07-06\lib\Python\Lib\subprocess.py", line 997, in _execute_child
startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
```
---
### Author:  [@jcfr](https://discourse.slicer.org/u/jcfr)
#### Post date: [July 10, 2019, 7:45am UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/10 "2019-07-10T07:45:57Z")
You should do this instead:
```auto
command_line=["F:/anaconda3/python.exe", "-c", "print('hola')"]
from subprocess import run
command_result = run(command_line, env=slicer.util.startupEnvironment())
print(command_result)
```
---
### Author:  [@Saima](https://discourse.slicer.org/u/Saima)
#### Post date: [July 11, 2019, 1:16pm UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/11 "2019-07-11T13:16:41Z")
> [@jcfr](#):
>
> command\_line=[“F:/anaconda3/python.exe”, “-c”, “print(‘hola’)”] from subprocess import run command\_result = run(command\_line, env=slicer.util.startupEnvironment()) print(command\_result)
the error remain the same
I am unable to understand.
It could not find the file.
---
### Author:  [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)
#### Post date: [July 11, 2019, 1:41pm UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/12 "2019-07-11T13:41:07Z")
@Saima I get the error you are getting when the python path that you are targeting doesn’t actually exist.
Can you confirm that `"F:\anaconda3\python.exe"` actually exists?
---
### Author:  [@Saima](https://discourse.slicer.org/u/Saima)
#### Post date: [July 11, 2019, 1:45pm UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/13 "2019-07-11T13:45:42Z")
yes I did installation again and the path was changed. I didnt check updated the path. now its running.
Thanks all
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [July 11, 2019, 2:25pm UTC](https://discourse.slicer.org/t/subprocess-call-does-not-work/2837/14 "2019-07-11T14:25:18Z")
FYI, since backslash (`\`) is an escape character in Python, you cannot simply use it in a string literal in Python.
The easiest is to indicate that you specify a raw string by prepending an `r` character before the string. This is correct:
```
somePath = r"F:\someFolder\python.exe"
```
If you need to use a regular string then backslash can be entered by typing double-backslash. This is correct:
```
somePath = "F:\\someFolder\\python.exe"
```
You may also use Unix-type separators. This is correct:
```
somePath = "F:/someFolder/python.exe"
```