Hi Bruce,
Thank you so much, sorry to replay so late.
I also read your conversation with Jonathan regarding 3D to 2D
transformation, it is very helpful.
On 06/22/2015 11:45 AM, Bruce Fischl wrote:
sure, the average subject has a sphere and you can do it there. Or you
can flatten and use euclidean coordinates
On Mon, 22 Jun 2015, xtong wrote:
Hi Bruce,
Thanks to your advise, the combination of mri_surf2surf my_subject ->
fsaverage(paint features to average brain) + mris_convert -c
*.ascii(output
features to ascii) works well, all my subjects can have the same
number of
vertice.
And it looks like the original xyz coordinate of my_subject can also be
passed to the average brain's vertices by mri_surf2surf2 --sval_xyz
--tval_xyz, which is terrific.
But beside vertex alignment another reason of wanting a 2D
representation of
the surface features (hence my ridiculous idea of creating template
for each
single subject), is to facilitate the random sampling of tiny sheets
from
the whole surface for my simulation study, since cutting a small
rectangular
(or other shape) from a picture is much easier than working on
vertices in
3D.
I found a solution by randomly selecting one vertex and retrieve it's
k-neighbour using the neighbour vertex table returned by mris_convert -v
fsaverage, it's still quite bit of work to be done though.
Is there any possibility to paint surface features to a picture in 2D
Longitude and Latitude coordinate?
Thank you so much.
On 06/20/2015 05:46 PM, Bruce Fischl wrote:
You probably don't need to create your own template - just use
mri_surf2surf to map the data (thickness, area, whatever) to
fsaverage and they will all have the same number of vertices
cheers
Bruce
On Sat, 20 Jun 2015, xiaoran tong wrote:
Dear FreeSurfer team:
I'm trying to model the cortical surface features
with a artificial neural
network. I need a uniformed number of input features
but it turns out the
vertices count varies from subject to subject.
Is that possible to map the vertices in the
Talairach space of XYZ to the
sphere template space of theta and phi, so I can
work on 2D pictures of
uniformed length and width? Probably 251 x 256 like
the FreeSurfer *.tif
template files.
According to
https://surfer.nmr.mgh.harvard.edu/fswiki/TemplateTifImageFiles
and
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
, I tried to create one registration template per
subject with
make_average_subject command in this manner:
make_average_subject --subjects sbj_i --out
sbj_i_template
, in the hope that I could at least extract the mean
curvature and convexity
of that subject in 2-D theta phe space from the
resulting sbj_i_template.tif
files.
It sounds ridiculous to call "make_average_subject"
on just every single
subject, but I couldn't think of any way to extract
vertex measures and in
the them 2D (theta, phi) space. I'm not sure this is
correct.
Beside curvatures, how should I extract other type
of vertex features, like
area, volume, and thickness in the 2D template
space?
I'll be thankful for any suggestions.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mai
l
contains patient information, please contact the Partners Compliance
HelpLin
e at
http://www.partners.org/complianceline . If the e-mail was sent to
you in er
ror
but does not contain patient information, please contact the sender
and prop
erly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
