it maps your functional data from the volume onto the surface model for
each individual subject (using the registration between the surface and the
functional data, usually computed with bbregister)
On Wed, 19 Mar 2014,
yufeng huang wrote:
Dear Bruce,
My last question: As I use the common surface-based coordinate system,
what the purpose of using mri_vol2surf for each individual at this time?
Did it register the functional data to the anatomical?
Thanks you very much for your attention!
Yufeng
2014-03-19 11:19 GMT-04:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
Hi Yufeng
can you remember to cc the list? And yes, if all you want is a
common surface-based coordinate system for your subjects then
there is no need for you to run mris_register yourself - it is
done by recon-all. All you need to do is run mri_vol2surf for
each individual, then map the resulting overlays to fsaverage
with mri_surf2surf
cheers
Bruce
On Wed, 19 Mar 2014, yufeng huang wrote:
Hi Bruce,
What does" rerun the registration - just use the
?h.sphere.reg files." mean?
Just using noting or using as follow code to produce new
?h.sphere.reg.newtemplate?
mris_register -curv surf/lh.sphere \
$SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
surf/lh.sphere.reg.newtemplate
2014-03-19 10:42 GMT-04:00 yufeng huang
<trista....@gmail.com>:
I want to do is map all the individual activation
maps into a
common surface-based coordinate system. So I do not
need to
follow the process of creating a registration
templatefromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemp
late
s) to do the surface-based registration.
1If I just use the ?h.sphere.reg which produce by recon-all.
But I
want to know : Who is the average subject at this time. The
fsaverage?
2 So at this time all I need to do is using mri_surf2surf onto
fsaverage surface? Or I should using mri_vol2surf first and do
the
mri_surf2surf next?
Thanks very much!
2014-03-19 9:46 GMT-04:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Yufeng
if all you want to do is map all the individual activation
maps into a common surface-based coordinate system,then
there is no need to create your own atlas and rerun the
registration - just use the ?h.sphere.reg files.
If there is some other reason you want to create your own
template/atlas, then you can check the results by using
make_average_subject to create a new version of
fsavverage, and mapping each subject's curvature file into
your new coordinate system using mri_surf2surf onto that
average subject's surface. Then see if they align. You
don't need to do anything about the inflated or other
surfaces. Use mri_vol2surf to map the data onto each
individual subject's surface, then mri_surf2surf with your
new registration file to map it to your new average
subject.
cheers
Bruce
On Wed, 19 Mar 2014, yufeng huang wrote:
Dear Burce,
I have 20 normal subjects, and I want to do
inter-subject surface-based
registration to all of them. So each one's
surface can align properly to the
other subject’s surface. After that I can put
the functional data onto the
surface which has aligned to each other
already.
And now I followed the process of creating a
registrationtemplatefromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRe
gAndTemp
late
s) to do the surface-based registration.
Round 1, all reference subjects
data are registered to the initial template,
producing ?h.sphere.myreg0.
(I've coordinated the suffix numbers with the
template used to produce the
registration.) Using that registration, a new
template (mytemp1.tif) is made
using all reference subjects as input. Round 2
is essentially a repeat of
Round 1, but produces an improved template
(mytemp2.tif) because Round 2's
initial registration step is based on a better
template than in Round 1.
I get the lh.sphere.reg.newtemplate1 and
rh.sphere.reg.newtemplate1 in
each subjects's surf folder. I do not know how
to check the result about if
every subject has aligned to each other
properly. And I do not know what
should I do next.
My question is :
1 How can I check about the result as if every
one has aligned each other
properly?
2 And what should I do next, I can not know if
the functional data can
aligned to the new surface properly. If I can
use mri_surf2surf or
mri_vol2surf can be used for this.
3 The lh.sphere.reg.newtemplate1 and
rh.sphere.reg.newtemplate1is just for
sphere, and how about the inflate aligned to
each other?
Yours Yufeng
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