Freesurfer segmentHA* and nipype

Dear everybody,

in freesurfer 7 the algorithm for hippocampal segmentation was changed.

As a result it is no longer possible to conveniently obtain it via ReconAll() with .inputs.hippocampal_subfields_T1 = True

Do you all use the command line now to manually initialize segmentation, or is there a workaround I am not aware of?

Thanks for your help!

Rudi K

Nipype’s ReconAll interface will have to be updated to handle FreeSurfer 7’s dependency graph. I’m not sure if they’ve published this (their wiki appears to be down).