Thank you, Bruce. For point 1, a nice alternative would be to be able to edit brainmask.mgz while T1.mgz is displayed instead. As for the control points, I generated one set in freeview, but when saving it with 'save as', it did not give me an option where to save it, and it did it in 'home' and not in subjid/tmp, so recon-all did not take it, I will try copy past that into the /tmp folder and retry. Is this a set path problem, and if so how can it be fixed.
thanks, Octavian On Sat, Nov 8, 2014 at 8:04 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > I'll leave 1 for Ruopeng. For 2, usuually I'll do a little cluster ofr 3-4 > together in an area, then a big space to the next cluster, but probably > even only 1 would be fine. 2-5mm is much denser than the cluster spacing > needs to be. For 3, yes that is fine > > > On Fri, 7 Nov 2014, Octavian Lie wrote: > > Dear all, >> >> I am editing recon-all segmentation results in freeview using the recon >> edit >> function. >> 1. Is there a way to complement the toggle between the brainmask.mgz and >> T1.mgz, especially at the end of pial editing, before resubmitting the >> saved >> brainmask volume to recon-all? It would be nice to be able to see the >> edited >> voxels (the final ones remaining edited, after successive >> deletions/clones) as a mask over the T1.mgz in freeview as the final check >> before sending brainmask back to segmentation. >> >> 2. As far as control points go, the FS tutorial mentions that there is a >> certain trial and error as to the no or density of control points to be >> used. Still, the example fig in the tutorial shows control points spaced >> about 2-5-voxels. Is this a good starting point in general? >> >> 3. Some of the segmentations need bit corrections in wm edits >> (filling holes), missing wm in brainmask (control points with T1.mgz as >> reference), and pial edits. It is OK if all of these corrections are done >> in a single step on brainmask.mgz with aux T1.mgz, then do >> recon-all -autorecon2-cp -autorecon3 -subjid? >> >> Thank you for your tips, >> >> Octavian >> >> > _______________________________________________ > 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. > >
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