Re: [Freesurfer] Making a custom experimental template

soft.join Huang wrote:

Hi doug,

I read your instructions on how to make an average subject, it looks quite streamlined. But I still have two questions about the procedure.

1. During the processing, every subject's surface need to register to

a common target, and where the target comes from, it is an existed template in FreeSurfer or randomly selected from the pool of subjects, or something else?

I would recommend starting off with fsaverage, then you can use your new average for the next iteration.

2. In order to get a well-established or accurate average template,

how many times does the function make_average_subject need to run?

I don't know for sure. Probably two iterations are enough.

doug

Thanks in advance, Lijie Huang

On Tue, May 10, 2011 at 3:28 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Joakim,

here are some instructions on what to do (some of which you've already
done):

doug

# Create an average subject (Creates $SUBJECTS_DIR/newtemplate)
make_average_subject --out newtemplate --subjects subj1 subj2
subj3 ...

# Register each subject to the new template (do for both lh and rh)
# Creates lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate
foreach subject (subj1 subj2 subj3 ...)
cd $SUBJECTS_DIR/subject
mris_register -curv surf/lh.sphere \
$SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
surf/lh.sphere.reg.newtemplate
end

# Get thickness values in the newtemplate space for GLM analysis
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s
subj3 ...

# Create another average template based on the previous one:
# (Creates $SUBJECTS_DIR/newnewtemplate)
make_average_subject --out newnewtemplate --surf-reg
sphere.reg.newtemplate \
--subjects subj1 subj2 subj3 ...




Joakim Vinberg wrote:
> Doug,
> Thanks! I just took a look at make_average_subject, and that looks
> quite a bit more streamlined--I think I'll just do that.
> Looking at make_average_subject, this should make the
replacement for
> fsaverage. Following that, I would want to run mri_surf2surf to
> generate all of the surfaces in our new template space?
> Thanks!
> Joakim
>
>
------------------------------------------------------------------------
> *From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>]
> *Sent:* Fri 5/6/2011 9:46 AM
> *To:* Joakim Vinberg
> *Cc:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Making a custom experimental template
>
> You are correct. If you run make_average_subject, it will create the
> template for you (as well as all the other files in a typical
subject
> dir -- you'll need these to do a simple replacement for fsaverage).
>
> doug
>
> Joakim Vinberg wrote:
> >
> > 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
> >
> >
------------------------------------------------------------------------
> >
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

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