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.andr...@kcl.ac.uk On 04/11/2015 11:33, "Andrews, Derek" <derek.andr...@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.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.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.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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
