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.andr...@kcl.ac.uk On 03/11/2015 17:41, "Douglas N Greve" <gr...@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.andr...@kcl.ac.uk >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >gr...@nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
