HELP

[LCC75]

Hi,
While testing sample data(CTabdomen) for segmentation, I got the following error:
Segmentation failed:
mm_segment failed with non-zero exit code.

Traceback (most recent call last):
File "", line 198, in run_module_as_main
File "", line 88, in run_code
File "E:\Users\lcc\anaconda3\Scripts\mm_segment.exe_main.py", line 2, in
File "E:\Downloads\PCL\MyDownload\download1 (2)\lib\Python\Lib\re_init.py", line 125, in
from . import _compiler, _parser
File "E:\Downloads\PCL\MyDownload\download1 (2)\lib\Python\Lib\re_compiler.py", line 18, in
assert _sre.MAGIC == MAGIC, "SRE module mismatch"
^^^^^^^^^^^^^^^^^^^
AssertionError: SRE module mismatch
I am on Windows 10 and using the stable release version Slicer 5.12.1

[Eddowesselink]

Hi @LCC75 ,

Thanks for the detailed traceback. Look at the two paths in your error:

running: E:\Users\lcc\anaconda3\Scripts\mm_segment.exe (Anaconda)
loading: E:\Downloads\PCL...\lib\Python\Lib\re_compiler.py (Slicer)

Anaconda's interpreter is starting up, but it's loading Slicer's standard
library. The compiled _sre module comes from Anaconda while _compiler.py comes
from Slicer, and those belong to different Python builds — that's what
"SRE module mismatch" means. Nothing is wrong with your data or your model.

We'll fix this on our side as well: the extension should launch these commands
with Slicer's startup environment (slicer.util.launchConsoleProcess with
useStartupEnvironment=True), so it works regardless of where mm_segment lives.

Before fixing anything, one quick check. Does Slicer's own
Python already have it?

dir "E:\Downloads\PCL\MyDownload\download1 (2)\lib\Python\Scripts\mm_*"

If mm_segment.exe is listed there, you don't need to install anything. Your
Anaconda copy is simply being found first on the PATH. Just rename it:

ren "E:\Users\lcc\anaconda3\Scripts\mm_segment.exe" mm_segment.exe.bak

Restart Slicer and try again — it will now pick up its own copy, which runs on
the same Python as Slicer, so the mismatch disappears. Renaming is fully
reversible; nothing is deleted.

If mm_segment.exe is NOT in that folder, then install it into Slicer's Python
instead.

Cheers,
Eddo