# How to run python script in Slicer?
**URL:** https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352
**Category:** Development
**Created:** [July 3, 2020, 8:13am UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352 "2020-07-03T08:13:26Z")
**Posts on this page:** 10
**Page:** 1
### Author:  [@SummerZ2020](https://discourse.slicer.org/u/SummerZ2020)
#### Post date: [July 3, 2020, 8:13am UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/1 "2020-07-03T08:13:26Z")
Operating system:Win10
Slicer version:4.11.0(2020.6.15)
Expected behavior:The saveLabel.py should be run when I run `C:\ProgramData\NA-MIC\Slicer 4.11.0-2020-06-15>Slicer.exe --python--script C:\Users\310091560\Desktop\saveLabel.py` in the command line window.
Actual behavior: nothing happened except the Slicer main window(python interactor) openning.
Is this command line `C:\ProgramData\NA-MIC\Slicer 4.11.0-2020-06-15>Slicer.exe --python--script C:\Users\310091560\Desktop\saveLabel.py` right to run a python script?
Thanks in advance.
BTW, is the tutorial “[[Documentation/Nightly/Extensions/DebuggingTools - Slicer Wiki](https://www.slicer.org/wiki/Documentation/Nightly/Extensions/DebuggingTools)]([http://Visual](http://Visual) Python debugging in PyCharm)” updated according to the 4.11 version? I cannot find the Python debugger extension and the “Python debugger” module (in “Developer Tools” category).
Thanks again.
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [July 3, 2020, 3:55pm UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/2 "2020-07-03T15:55:40Z")
> [@SummerZ2020](#):
>
> C:\ProgramData\NA-MIC\Slicer 4.11.0-2020-06-15\>Slicer.exe --python–script C:\Users\310091560\Desktop\saveLabel.py
The correct argument name is `--python-script` and not `--python--script`.
---
### Author:  [@SummerZ2020](https://discourse.slicer.org/u/SummerZ2020)
#### Post date: [July 8, 2020, 1:39am UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/3 "2020-07-08T01:39:49Z")
So simple mistake, I should be more careful. Thanks a lot.
---
### Author:  [@Gokce\_Guven](https://discourse.slicer.org/u/Gokce_Guven)
#### Post date: [July 30, 2023, 8:18pm UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/4 "2023-07-30T20:18:14Z")
Hi Mr. Lasso,
I am trying to run a python script from Slicer 5.3.0 version on Ubuntu 22.04 OS. When I run it from the terminal like this:
./Slicer --python-script /home/username/ls.py
it gives this error eventhough I have tkinter on my system:
/lib/python3.9/ls.py
Switch to module: “Welcome”
Loading Slicer RC file [/home/gokce/.slicerrc.py]
:1: DeprecationWarning: The symbol module is deprecated and will be removed in future versions of Python
NOTE: You must install tkinter on Linux to use MouseInfo. Run the following: sudo apt-get install python3-tk python3-dev
Switch to module: “”
Switch to module: “”
When I put the ls.py script inside the folder: /home/username/Slicer-5.3.0-2023-07-29-linux-amd64/lib/Python/lib/python3.9/ folder and start the slicer and import the ls script from the python console and call a function from the ls script it gives this error:
```auto
>>> import ls
>>> ls.start()
File "", line 1
import ls
^
SyntaxError: multiple statements found while compiling a single statement
>>>
```
How should I proceed?
Thanks in advance
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [July 31, 2023, 1:11am UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/5 "2023-07-31T01:11:29Z")
Slicer uses its own virtual Python environment (you don’t need to install Python in your system). If you want to install a package in Sicer’s virtual Python environment then you can use the `pip_install` convenience function in the Slicer Python console.
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [July 31, 2023, 2:27am UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/6 "2023-07-31T02:27:07Z")
`SyntaxError: multiple statements found while compiling a single statement` error means that statements are not separated by newline or semicolon (`;`). Maybe during copy-paste, the newline character gets replaced by a space? You may try to copy-paste from a different software or add semicolon after each statement (`import ls; ls.start()`).
I would not recommend to put any files into the Python library folder (`/home/username/Slicer-5.3.0-2023-07-29-linux-amd64/lib/Python/lib/python3.9/`). Instead you can put it anywhere and run it by calling as you did (`./Slicer --python-script /home/username/ls.py`). You can ignore the deprecation warning. When Slicer will upgrade to a Python version that does not contain tkinter anymore (or even before that) you can switch to Qt, which is already bundled with Slicer.
---
### Author:  [@Gokce\_Guven](https://discourse.slicer.org/u/Gokce_Guven)
#### Post date: [July 31, 2023, 8:00am UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/7 "2023-07-31T08:00:55Z")
Dear Mr. Lasso, thanks a lot for the detailed and fast response. When I run it from the terminal like this:
```auto
./Slicer --python-script ../ls.py
Switch to module: "Welcome"
Loading Slicer RC file [/home/gokce/.slicerrc.py]
:1: DeprecationWarning: The symbol module is deprecated and will be removed in future versions of Python
NOTE: You must install tkinter on Linux to use MouseInfo. Run the following: sudo apt-get install python3-tk python3-dev
Switch to module: ""
Switch to module: ""
```
I forgot to add that the slicer is opening for a second and closing itself. The ls.py script is using lung segmenter plugin in slicer and the same code is working on Windows. I want to run it on Ubuntu 22.04.2, I do not know what is wrong. I have tried many possible solutions that I have found on web. When I call the code from the python console without space like this:
```python
Python 3.9.10 (main, Jul 30 2023, 03:07:06)
[GCC 7.3.1 20180303 (Red Hat 7.3.1-5)] on linux2
>>>
Loading Slicer RC file [/home/username/.slicerrc.py]
>>> import ls;ls.start()
>>>
```
it is not giving any output, I cannot understand what may be possibly wrong.
---
### Author:  [@Gokce\_Guven](https://discourse.slicer.org/u/Gokce_Guven)
#### Post date: [July 31, 2023, 10:45am UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/8 "2023-07-31T10:45:56Z")
@lassoan Hi Mr. Lasso,
I have tried to comment out one of my python package “pyautogui” and uninstall it from the Slicer, then my code worked. I wanted to take screenshots of the segmentation for each data with pyautogui. Do you have any suggestion for collecting the screenshots for each data?
Thanks in advance
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [July 31, 2023, 11:46am UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/9 "2023-07-31T11:46:46Z")
You can use the Screen Capture module to take screenshots. See the [script repository](https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#screen-capture) for examples.
---
### Author:  [@Gokce\_Guven](https://discourse.slicer.org/u/Gokce_Guven)
#### Post date: [July 31, 2023, 12:36pm UTC](https://discourse.slicer.org/t/how-to-run-python-script-in-slicer/12352/10 "2023-07-31T12:36:06Z")
thanks a lot Mr. Lasso, that solved my problem
Have a great day