Re: [Freesurfer] custom templates and mris_make_template options

you could do it different ways, but we always start with the lh.sphere to try to find the minimally distorting transformation.

Bruce

On Sun, 24 Aug 2008, Jan Kalkus wrote:

Thanks Bruce,

One more question, just to be sure, when using mris_register, the first time I use:

mris_register \ -curv \ $SUBJECTS_DIR/bu_edited/surf/lh.sphere \ lh.monk_temp_wreg1.tif \ $SUBJECTS_DIR/bu_edited/surf/lh.sphere.reg

Is this correct? I shouldn't be using *h.sphere.reg (instead of *h.sphere) for the input surface after the first round?

Thanks.

• Jan Kalkus

On Aug 24, 2008, at 10:15 PM, Bruce Fischl wrote:

...

Hi Jan,

you should use the ?h.sphere.reg on the 2nd round. On our 1st round we use a single subject ?h.sphere to avoid blurring the folding patterns too much, then register all to that one, create the atlas from all the subjects (with the sphere.reg), then recreate all the sphere.reg by reregistering to the 2nd round atlas, then create a 3rd round atlas from the new sphere.reg files.

let us know if you need more help.

Bruce

On Sun, 24 Aug 2008, Jan Kalkus wrote:

...

Hi everyone,

We're making a template to register some monkey brain surfaces to. I've written a script based on instructions from the Surface Registration and Templates page ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) on FreeSurfer wiki. I'm stuck at "Round 1" with the "mris_make_template" command. In the first step we used:

mris_make_template \
lh sphere \
bu_edited bs_edited vi_edited \
lh.monk_temp_all.tif

As there were no *h.sphere.reg files yes, we used the *h.phere surfaces. My question is, for the next "mris_make_template" should we use the same (*h.sphere) surface or use the newly created *h.sphere.reg surfaces to create the template?

mris_make_template \
lh sphere.reg \
bu_edited bs_edited vi_edited \
lh.monk_temp_all.tif

Has anyone else used this process to create their own templates/registered surfaces? Does anyone have any suggestions? Thanks.

• Jan Kalkus

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