FreeSurfer v6.0 entorhinal cortex labeling

[effigies]

Summary

In FreeSurfer v6.0 (release candidate), -(no)label-exvivo-ec are no longer valid options. Entorhinal cortex labeling appears to be done by -balabels (see the final line of the recon-all table).

I'm guessing the solution will be to check $FREESURFER_HOME/build-stamp.txt for the version and modify ReconAll._steps accordingly.

Actual behavior

'-(no)label-exvivo-ec' options are added to the ReconAll cmdline.

Expected behavior

'-(no)label-exvivo-ec' options are omitted for FreeSurfer v6.0+.

How to replicate the behavior

1. Install FreeSurfer v6.0:

curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-release-candidate/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz \
    | tar zx -C /opt \
    --exclude='freesurfer/trctrain' \
    --exclude='freesurfer/subjects/fsaverage_sym' \
    --exclude='freesurfer/subjects/fsaverage3' \
    --exclude='freesurfer/subjects/fsaverage4' \
    --exclude='freesurfer/subjects/fsaverage5' \
    --exclude='freesurfer/subjects/fsaverage6' \
    --exclude='freesurfer/subjects/cvs_avg35' \
    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
    --exclude='freesurfer/subjects/V1_average' \
    --exclude='freesurfer/average/mult-comp-cor' \
    --exclude='freesurfer/lib/cuda' \
    --exclude='freesurfer/lib/qt'

2. Place license file in /opt/freesurfer/license.txt

3. Run ReconAll on bert:

>>> import os
>>> from nipype.interfaces.freesurfer import ReconAll
>>> interface = ReconAll(subject_id='bert', directive='all', subjects_dir=os.getenv('SUBJECTS_DIR'))
>>> 'label-exvivo-ec' in interface.cmdline
True

Platform details:

{'commit_hash': '<not found>',
 'sys_platform': 'linux',
 'networkx_version': '1.11',
 'commit_source': '(none found)',
 'numpy_version': '1.11.3',
 'sys_executable': '/usr/local/miniconda/bin/python',
 'nibabel_version': '2.1.0',
 'traits_version': '4.6.0',
 'sys_version': '3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:53:06) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]',
 'scipy_version': '0.18.1',
 'pkg_path': '/usr/local/miniconda/lib/python3.5/site-packages/nipype'
}

[effigies]

@satra Any opinion on the best way forward, here?

I suppose the first question is: Is ReconAll superseded by workflows.smri.freesurfer.create_reconall_workflow? Since that was designed with FreeSurfer 6 in mind, I don't want to waste too much time retrofitting ReconAll if it's due to be deprecated.

[anbai106]

Hi, so I had the same issue with FreeSurfer v6.0 on my linux workstation, but not on my Mac, so what is the solution? What do you mean ReconAll should be deprecated? you mean we should just use workflows.smri.freesurfer.create_reconall_workflow instead?

[effigies]

This should have been resolved in 0.13.1. What version of nipype do you have installed?