Dear Bruce,

It worked, I transferred it and is ready for view.

The original recon was with the command
recon-all -3T -openmp 8 -notal-check (the raw volume was analyze).

I noted a small gyrus excluded from the surfaces, located in the right hemisphere posteriorly; the recon also did not include two other regions in the left hemisphere (one mesial gyrus, and a wedge-shaped region, also posteriorly located), but I am insterested mainly in the right hemisphere, and I suspect the solution would be the same.

After the original recon, I did some pial editing (although not perfect), and tried control points and wm/topological defect corrections. As suchs, the wm.mgz included was edited to extend into the excluded areas for correction.

Thank you for helping, as always. Please let me know if there is a fix, such as cloning voxels from T1.mgz into brain.finalsufs,manedit.mgz.

Octavian

On Mon, Nov 10, 2014 at 11:09 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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
> > <rightgyrusfailure.png>
> > <rightgyrusfailurewm.png>
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