Unknown version string with Freesurfer 7

[0rC0]

Summary

After update to freesurfer 7 import nipype.interfaces.freesurfer returns RuntimeError: Unknown version string error.

Actual behavior

$ python
Python 3.8.2 (default, May  7 2020, 20:00:49) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from nipype.interfaces.freesurfer import Info
200518-18:18:10,4 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/anaconda3/envs/neuromet_dev/lib/python3.8/site-packages/nipype/interfaces/freesurfer/__init__.py", line 7, in <module>
    from .preprocess import (
  File "/opt/anaconda3/envs/neuromet_dev/lib/python3.8/site-packages/nipype/interfaces/freesurfer/preprocess.py", line 36, in <module>
    FSVersion = Info.looseversion().vstring
  File "/opt/anaconda3/envs/neuromet_dev/lib/python3.8/site-packages/nipype/interfaces/freesurfer/base.py", line 80, in looseversion
    raise RuntimeError("Unknown version string: " + ver)
RuntimeError: Unknown version string: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b

How to replicate the behavior

1. Install Freesurfer 7 as described here with Freesurfer from here (file: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz.
2. create a fresh new conda environment with
   conda create -n $name python=3.8 nipype
3. open python and try to import 'nipype.interfaces.freesurfer`

Platform details:

$cat /etc/lsb-release 
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
DISTRIB_DESCRIPTION="Ubuntu 16.04.6 LTS"

$python -c "import nipype; from pprint import pprint; pprint(nipype.get_info())"
200518-18:29:34,82 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
{'commit_hash': '%h',
 'commit_source': 'archive substitution',
 'networkx_version': '2.4',
 'nibabel_version': '3.1.0',
 'nipype_version': '1.5.0-rc1',
 'numpy_version': '1.18.1',
 'pkg_path': '/opt/anaconda3/envs/neuromet_dev/lib/python3.8/site-packages/nipype',
 'scipy_version': '1.4.1',
 'sys_executable': '/opt/anaconda3/envs/neuromet_dev/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.8.2 (default, May  7 2020, 20:00:49) \n[GCC 7.3.0]',
 'traits_version': '5.2.0'}

Execution environment

Choose one

• My python environment outside container

[liamtimms]

I can confirm this in my environment as well. My solution is to hold off on the Freesurfer update for now.

[0rC0]

As (naive :P) workaround to test Freesurfer 7, I've put on line 80 of /opt/anaconda3/envs/neuromet_dev/lib/python3.8/site-packages/nipype/interfaces/freesurfer/base.py in my test environment

return LooseVersion("0.0.0")

instead of

raise RuntimeError("Unknown version string: " + ver)

My recon-all routine failed by the hippocampal subfield module, because it is now in separates scripts.

ERROR: the hippocampal subfield module is now in separate scripts:
  segmentHA_T1.sh
  segmentHA_T2.sh
  segmentHA_T1_long.sh