Dear FreeSurfer support team,
It appears that ‘zcat’ appears in line 126 of the load.mgh script, I have changed this to gzcat which appears to have solved the issue.
Again, thank you for your support. It is very 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
On 04/11/2015 11:33, "Andrews, Derek" derek.andrews@kcl.ac.uk wrote:
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.pia l .filled.mgz
(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pi a 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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