load_mgh.m and load_nifti.m in $FREESURFER_HOME/matlab On 11/04/2015 06:33 AM, Andrews, Derek 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.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 > >
-- 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
