yes, that is correct. All that info is generated as a matter of course during recon-all.

Bruce On Tue, 6 Oct 2009, Xiaojing Long wrote:

Hi, Bruce,

Thank you so much for your help.

Now my understanding on 'mris_register' is that£º

1. I need to construct the 'xx.sphere' for all my inputs;
2. For the 'source.sphere', I also need to provide 'source.curv' and 'source.sulc'.
3. For the 'target.sphere', I need to have a statistical file (i.e. xh.average.curvature.filled.buckner40.tif). If the target is not a template/atlas, I need to create the tif file for that single subject.

Am I right? If so, how can I input all these information? Using the optional arguments?

Thank you again.

Best, Xiaojing

2009/10/6 Bruce Fischl fischl@nmr.mgh.harvard.edu

...

Hi Xiaojing,

the inputs are an individual subject sphere created with mris_sphere, and statistics in an atlas coordinate system, usually stored in a tif file that we supply.

cheers, Bruce

On Tue, 6 Oct 2009, Xiaojing Long wrote:

Hi, all,

...

I am new to FreeSurfer world. I am trying to do the surface-based registration using FreeSurfer. I found a tool called mris_register, which is defined as a command registering a surface to an average surface template(or another single-subject's surface). But I don't understand how to use this command.

Are the inputs often xx.sphere? I have two wm surfaces 'subj1.smoothwm' and 'subj2.smoothwm' and I want to align them. Can I use mris_register to do that? What information or parameterization are required by mris_register? Since when I run this command, I get errors saying that: "reading template parameterization from target.smoothwm HIPS unsupported No such file or directory"

I don't understand what this error means. Could anyone help me? Thank you so much.

Best, Xiaojing

Hi, Douglas,

Thank you so much for your help.

I once ran the recon-all for my subjects and I got the 'xx.sphere.reg's. Are these results the warped sphere surfaces to the atlas?

I am trying to register the wm surface of subject1 to surface of subject2, so I am seeking for help to use 'mris_register'. Can I use another tool to do that?

Thank you again.

Best, Xiaojing

2009/10/6 Douglas N Greve greve@nmr.mgh.harvard.edu

The surface-based registration is usually done as part of recon-all (which runs mris_register with all the appropriate arguments). You trying to do something different?

doug

Xiaojing Long wrote:

...

Hi, all, I am new to FreeSurfer world. I am trying to do the surface-based registration using FreeSurfer. I found a tool called mris_register, which is defined as a command registering a surface to an average surface template(or another single-subject's surface). But I don't understand how to use this command. Are the inputs often xx.sphere? I have two wm surfaces 'subj1.smoothwm' and 'subj2.smoothwm' and I want to align them. Can I use mris_register to do that? What information or parameterization are required by mris_register? Since when I run this command, I get errors saying that: "reading template parameterization from target.smoothwm HIPS unsupported No such file or directory" I don't understand what this error means. Could anyone help me? Thank you so much. Best, Xiaojing

---

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Thank you all so much.

I will first try to figure out how 'mris_register' works for registering a subject to the atlas. Then think about my problem.

Best, Xiaojing

2009/10/6 Bruce Fischl fischl@nmr.mgh.harvard.edu

there is -1 switch you can give mris_register to directly register one surface to another, but in our experience using the atlas statistics and the measures of cross-subject variability stabilizes the whole procedure

On Tue, 6 Oct 2009, Xiaojing Long wrote:

Hi, Douglas,

...

Thank you so much for your help.

I once ran the recon-all for my subjects and I got the 'xx.sphere.reg's. Are these results the warped sphere surfaces to the atlas?

I am trying to register the wm surface of subject1 to surface of subject2, so I am seeking for help to use 'mris_register'. Can I use another tool to do that?

Thank you again.

Best, Xiaojing

2009/10/6 Douglas N Greve greve@nmr.mgh.harvard.edu

The surface-based registration is usually done as part of recon-all (which

...

runs mris_register with all the appropriate arguments). You trying to do something different?

doug

Xiaojing Long wrote:

Hi, all,

...

I am new to FreeSurfer world. I am trying to do the surface-based registration using FreeSurfer. I found a tool called mris_register, which is defined as a command registering a surface to an average surface template(or another single-subject's surface). But I don't understand how to use this command. Are the inputs often xx.sphere? I have two wm surfaces 'subj1.smoothwm' and 'subj2.smoothwm' and I want to align them. Can I use mris_register to do that? What information or parameterization are required by mris_register? Since when I run this command, I get errors saying that: "reading template parameterization from target.smoothwm HIPS unsupported No such file or directory" I don't understand what this error means. Could anyone help me? Thank you so much. Best, Xiaojing

---

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting