Hello Freesurfer Support Team,

I have encountered an issue running recon-all –lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like this…

>> reading filled volume...

zcat: can't stat: /Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz (/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.Z): No such file or directory

Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script).

Any suggestions or work throughs would be appreciated.

Best, Derek 

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Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences 

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: Derek.Andrews@kcl.ac.uk