Dear Douglas,
Thank you for response. To clarify, I need to find out where in the lGI scripts zcat is being called so that I can change the code to use something like gunzip.
Best, Derek
________________________________________ 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
On 03/11/2015 17:41, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
you can find out where it is with which zcat
On 11/03/2015 07:42 AM, Andrews, Derek wrote:
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 thisŠ
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.pia l.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
*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
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