try changing the local dir to /usr/local/fs5.3/freesurfer/subjects and just putting the file without a path
cheers Bruce On Mon, 10 Nov 2014, Octavian Lie wrote: > Thank you, Bruce > > I tried to upload the subject (tar.gz, 183 Mb) to the ftp, followed > instructions > > ftp surfer.nmr.mgh.harvard.edu > anonymous > my email > cd transfer/incoming > put /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz > > and I get this: > > local: /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz remote: > /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz > 200 PORT command successful. Consider using PASV. > 553 Could not create file. > > Please advise, > > Octavian > > On Sun, Nov 9, 2014 at 9:44 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > Hi Octavian > If you upload the subject we will take a look > Cheers > Bruce > > > > > On Nov 9, 2014, at 10:40 PM, Octavian Lie > <octavian....@gmail.com> wrote: > > > > Dear all, > > > > 1. in the attached there is a gyrus that does not incorporated > into surfaces, whatever I do (wm edits/topological > defects-cloning voxels from brainmask.mgz or T1.mgz into wm.mgz, > save volume then run recon-all autorecon2-wm autorecon 3), or > control points addition to wm in brainmask.mgz, then run the -cp > flag. Is there any other solution left to clone the white matter > (and pial voxels) left out? is brain.finalsurfs.manedit.mgz a > solution? > > > > 2. Unrelated, after manual pial edits and reruning the > recon-all autorecon-pial command, the pial surface generated is > mostly OK, however where there have been heavy dura editing the > surface looks granular. Is there a workaround (along with better > hands), such as smoothing the final pia a bit more (preferably > in the recon-all pipeline as to be convergent with other > segmentation results). > > > > I appreciate your help, > > > > Octavian > > <rightgyrusfailure.png> > > <rightgyrusfailurewm.png> > > _______________________________________________ > > 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 > > > 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
