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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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