Re: [Freesurfer] edit failure

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 fischl@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.lie@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

...

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