The first cmd (mris_register, or use the surfreg script) will create a new registration file in subject/surf. Make sure you don't overwrite the original one (?h.sphere.reg). mris_preproc will just create a single output file with all of your subjects' thickness data (unless you use --qcache) doug

On 02/18/2013 05:58 AM, Sophie Maingault wrote:

Hello,

Thank you for your answer. I found this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates

So I have to do the point “Creating a registration template initialized with FreeSurfer template (DG)” : first the command mris-register –curv and then mris_preproc –surfreg ? But what type of file it will create ? In the directory surf ? It will change the parcellation ?

Cheers

Sophie

---

*De :*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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: [Freesurfer] Recon-all with my own template

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 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 current one (if it wasn't you wouldn't be able to use our cortical parcellations)

cheers Bruce

On Fri, 15 Feb 2013, Sophie Maingault wrote:

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 new template in the subject_dir ?

Thank you for the answer !

Sophie

---

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