Dear FreeSurfer experts,
I am trying to create an average subject based on a matched subsample (2 different scanners, patients and healthy controls).
I successfully ran make_average_subject receiving a "newtemplate". Now I am unsure how to proceed:
As far as I understand it, according to the SurfaceRegAndTemplates page (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) I should use mris_register for each subject from my subsample receiving ?h.sphere.reg.newtemple files with which I should make again an average subject, let's call it "newnewtemplate".
Is that correct?
Now, if I want to assemble the data into common space using mris_preproc: what do I need to specify? Would --target be the newtemplate or newnewtemplate? Do I need to specifiy the --surf-reg as well?
On the other hand, I read in one of your tutorials that I only need to run make_average_subject receiving a "newtemplate" which I then specify using mris_preproc as --target and that --surf-reg is not needed.
So what would be the correct way to use my own template for the group analysis?
Many thanks for you help!
Best wishes Christina
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Christina Schuster, M.Sc.
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Standort Rostock/ Greifswald Sitz am Zentrum für Nervenheilkunde (über Station N4) Gehlsheimer Straße 20 D- 18147 Rostock Tel: +49-381-494-9618 Fax: +49-381-494-9472 E-mail: christina.schuster@dzne.de Web: http://www.dzne.de
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Vorstand: Prof. Pierluigi Nicotera, MD PhD (Vorstandsvorsitzender und wissenschaftliches Vorstandsmitglied) und Ursula Weyrich (administratives Vorstandsmitglied) eingetragen in das Vereinsregister des Amtsgerichts Bonn (Az. VR 9021)
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Hi Christina,
the new template will already be in the same target space as fsaverage since you used the sphere.reg to create it. Just use it as a background for your group results.
cheers Bruce
On Thu, 31 May 2012, Schuster, Christina /DZNE wrote:
Dear FreeSurfer experts,
I am trying to create an average subject based on a matched subsample (2 different scanners, patients and healthy controls).
I successfully ran make_average_subject receiving a "newtemplate". Now I am unsure how to proceed:
As far as I understand it, according to the SurfaceRegAndTemplates page (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) I should use mris_register for each subject from my subsample receiving ?h.sphere.reg.newtemple files with which I should make again an average subject, let's call it "newnewtemplate".
Is that correct?
Now, if I want to assemble the data into common space using mris_preproc: what do I need to specify? Would --target be the newtemplate or newnewtemplate? Do I need to specifiy the --surf-reg as well?
On the other hand, I read in one of your tutorials that I only need to run make_average_subject receiving a "newtemplate" which I then specify using mris_preproc as --target and that --surf-reg is not needed.
So what would be the correct way to use my own template for the group analysis?
Many thanks for you help!
Best wishes Christina
Christina Schuster, M.Sc.
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Standort Rostock/ Greifswald Sitz am Zentrum für Nervenheilkunde (über Station N4) Gehlsheimer Straße 20 D- 18147 Rostock Tel: +49-381-494-9618 Fax: +49-381-494-9472 E-mail: christina.schuster@dzne.de Web: http://www.dzne.de
Vorstand: Prof. Pierluigi Nicotera, MD PhD (Vorstandsvorsitzender und wissenschaftliches Vorstandsmitglied) und Ursula Weyrich (administratives Vorstandsmitglied) eingetragen in das Vereinsregister des Amtsgerichts Bonn (Az. VR 9021)
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Bruce Fischl -
Schuster, Christina /DZNE