External Email - Use Caution        

No problem Georgios,

It’s easily done. I’ll check if we can streamline the patching process.

I’ve written a bit of an explanation below in case you or anyone else on the 
freesurfer list comes across a problem like this again.

Best wishes,
Henry

===========================

Explanation:
Many of the network-based tools in freesurfer are distributed as python scripts 
which build a tensorflow or pytorch network, load the model weights from 
$FREESURFER_HOME/models and push the data through. As changing the combination 
of python package versions can have unexpected effects, freesurfer comes with 
its own python environment “fspython”. For these python-based tools the files 
in $FREESURFER_HOME/bin are shell scripts that run some checks then pass the 
python scripts in $FREESURFER_HOME/python/scritps and any arguments to the 
fspython environment.

In this case replacing the file in the bin directory with the python code 
likely meant it was running in your local python environment using different 
package versions. A clue to this is the deprecation warning mentioning numpy 
version 1.25 as the version in fspython is 1.24.3

From: Georgios Argyropoulos <gargyropou...@gmail.com>
Date: Thursday, 11 April 2024 at 17:24
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>, Tregidgo, 
Henry <h.tregi...@ucl.ac.uk>
Subject: Re: [Freesurfer] Question on using thalseg_1.1.h5

⚠ Caution: External sender

Many thanks and apologies, Henry - I figured it out... I stupidly replaced your 
improved segmentation script in both the scripts and the bin directory instead 
of only replacing the former.

many thanks for your time, much appreciated

g
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