External Email - Use Caution
Hello,
I encountered two reproducible bugs in the latest release, Stable 8.2.0 (March 18 2026), when running recon-all with an expert options file on a 0.7 mm 7T MP2RAGE dataset.
First, the run crashes after mris_sphere because recon-all evaluates if($XOptsFile), which expands to the expert-options path and triggers tcsh’s "if: Expression Syntax." error. A suggested fix would be to replace if($XOptsFile) with if($#XOptsFile).
After patching this locally, recon-all proceeds further but then passes --expert to rca-surfreg, which currently recognizes -expert but not --expert, causing a second crash with "ERROR: Flag --expert unrecognized". A suggested fix would be to add support for --expert in rca-surfreg, for example: case "--expert": case "-expert": These issues were reproduced with an expert options file containing only mris_inflate -n 60. I have also registered the bug on GitHub and am emailing here for completeness.
Best regards,
Sophocles Goulis
Postdoctoral Research Fellow
Max Planck UCL Centre for Computational Psychiatry and Ageing
Department of Imaging Neuroscience
UCL Queen Square Institute of Neurology
University College London, London, UK