Hi Guang,

sorry, it's hard to parse your email. The procedure is

mris_make_template one_subject one_subject.tif

run mris_register on all subjects with one_subject.tif as the target mris_make_template $ALL_SUBJECTS all_subjects.tif run mris_register on all subjects with all_subjects.tif as the target mris_make_template $ALL_SUBJECTS all_subjects.tif

cheers Bruce

On Sun, 15 Nov 2009, Guang Zeng wrote:

Hi, there,

I am creating our own template now, and stucked at "Round 1" now (based on FreeSurfer WIKI description http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates). I found a thread posted a year ago and asked the same kind of question, (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08028.html) I read the thread, but still have three questions.

I pasted part of the thread here;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% "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 \                              [Command. 1]
           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 \                            [Command. 2]


           lh.monk_temp_all.tif"

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Question. 1,

...

From my understanding, their template include three subjects "bu_edited", "bs_edited", "vi_edited", and their command. 1 actually is what FreeSurfer WIKI called "Prep" step.

However, I think in this step, only one subject is needed to create the template "lh.monk_temp_all.tif", am I right ?

Actually, Bruce also mentioned that a single subject is used in 1st round, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Question. 2,

In round. 1, we need call mris_make_template again using all the reference subjects. I think their command. 2 is written for this. However, is this command line correct? I thought it may looks like this: [Command. 3]

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

So which one is correct?

Actually, I tried both of them, they all worked. The only difference is the file size of lh.monk_temp_all.tif from Command.2 (1.3 M) is half of the result from Command. 3. (2.7M)

Question. 2, If we correctly creat our template, and load it use MATLAB, will the size of the .tif file be 512 x 256 x 9? currently, when I load my .tif files, they are all 512 x 256.

Thanks a lot for your help!

Guang

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