Hi FS crowd,

I just want to make sure that I have the process correctly described for setting up a custom experimental template. I am basing this off of the SurfaceRegAndTemplates (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates), and a hypothetical experiment with 10 subjects (s1, s2, …s10). I apologize if this has been well-covered—I couldn’t quite match it on the website or the archives.

For the prep step, I believe my commands would be:

mris_make_template lh sphere s1 custom_template_lh_0.tif

mris_make_template rh sphere s1 custom_template_rh_0.tif

which would result in two new template files names custom_template_lh_0.tif and custom_template_rh_0.tif

For Round 1, I would first create another registration for each subject:

mris_register s1/surf/lh.sphere custom_template_lh_0.tif s1/surf/lh.sphere.regcustom_0

mris_register s1/surf/rh.sphere custom_template_rh_0.tif s1/surf/rh.sphere.regcustom_0

…

mris_register s10/surf/lh.sphere custom_template_lh_0.tif s10/surf/lh.sphere.regcustom_0

mris_register s10/surf/rh.sphere custom_template_rh_0.tif s10/surf/rh.sphere.regcustom_0

And then create another custom template:

mris_make_template lh sphere s1 s2 s3 … s10 custom_template_lh_1.tif

mris_make_template rh sphere s1 s2 s3 … s10 custom_template_rh_1.tif

For round 2, I would repeat Round 1, generating a new set of sphere.reg files, and then a new template, except substitute the custom template from round 1 (custom_template_lh_1.tif and custom_template_rh_1.tif).

Then, I would register all of my data to the custom_template_lh_2.tif and custom_template_rh_2.tif generated at the end of round 2. From there, I am assuming that I could be able to use this new template as I would fsaverage. Am I correct, or have I missed a step?

Thanks in advance for all of your help!

Joakim