Re: [Freesurfer] Recon-all with my own template

2013-02-25 Thread Douglas N Greve
--- > > *De :*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *De la p**art > de*Douglas Greve > *Envoyé :* vendredi 15 février 2013 18:02 > *À :* freesurfer@nmr.mgh.harvard.edu > *Objet :* Re: [Freesurfe

Re: [Freesurfer] Recon-all with my own template

2013-02-15 Thread Douglas Greve
You can also register your subjects to the new average subject (creates a new spherical registragtion). Use the surfreg script (run with --help for more info). doug On 2/15/13 8:55 AM, Bruce Fischl wrote: Hi Sophie what template do you mean? You can't rerun the subcortical segs or parcella

Re: [Freesurfer] Recon-all with my own template

2013-02-15 Thread Bruce Fischl
Hi Sophie what template do you mean? You can't rerun the subcortical segs or parcellations since they depend on manual labelings. You could regenerate our cortical folding patterns atlas, but I don't think that buys you much since the atlas you would build is by definition in register with our

[Freesurfer] Recon-all with my own template

2013-02-15 Thread Sophie Maingault
Hello Freesurfer experts ! I created a new template with make_average_subject called 80tvs and I would like to re-run some of my subjects with this new template. I can't find the command line in FAQ. Is it for example : recon-all -all -s t0001 -target 80tvs ?? So I need the repertory of this ne