Hi Donna,
Thank you very much for your quick reply. My current application is
on a small sample of subjects (n<8), and we just want to average
some individual maps in the PALS atlas space. This is a supplementary
analysis to the main ROI-based analysis, which is something I do most
of the time, so my question may sound naive. Please bear with me :)
Thanks for the pointer about the menu. I can now inflate my own
surface (I didn't search hard enough, I guess). I'm going to follow the
tutorial to see how the whole thing works. In the mean time, I have a
few more questions.
1. So what's the purpose of smoothing the medial wall? Do I need to
do this given my purpose? Is there some instruction on how to do this?
I don't seem to see this step in the tutorial.
2. I read the link you sent me. I'm interested in drawing the
landmarks without using the flat surface. Do you recommend this? I
don't really need to flatten, I guess. It'll be fine to visualize the
final result on a inflated surface. The instruction
(http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html/)
seem to suggest it's less accurate to draw it on the spherical surface,
which I agree; it's hard to know what is what there. But can I draw it
on the very inflated one? Seems it'll be easier to draw it there.
3. One of the links mentioned that the volume should be normalized
to standard space. I generally don't do any normalization. Do you think
it's a problem for my purpose? I'm thinking as long as I register each
subject's brain surface to the atlas surface, that should be ok. It'll
be a bit hard for me to do this as my software doesn't currently
support normalization (again, coming from a ROI-based tradition).
In general, I would like to have relatively high accuracy in my
spherical registration. And given my small sample, I don't mind doing
things manually. Could you advise the best thing to do? Sorry some of
the questions might be obvious if I follow through the tutorial but I'm
just a bit overwhelmed by the software right now (it's an awesome
software, that's why I'm trying to learn it).
Thank you so much,
--taosheng
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Today's Topics:
1. Caret newbie question:spherical registration (Taosheng Liu)
2. Re: Caret newbie question:spherical registration (Donna Dierker)
Hello,
I'm new to Caret and I'd like to run spherical registration to the
atlas and do group analysis. Most of my analysis is done in custom
Matlab codes. I use a combination of FreeSurfer and SurfRelax (a less
used software) to do segmentation and surface recon.
I'm able to output my surface to Caret fomat, i.e., I can generate
topo and coords files for a folded hemisphere, and open/visualize them
in Caret. I tried to follow the Caret_5.5_Tutorial_Segment.pdf for
doing registration, but I'm currently stuck, because it seems to
require flattened/inflated/spherical surfaces of my subjects.
I'm imagining that I can start with my folded surface and do all those
things, and then follow the tutorial to do spherical registration? My
question for now is simply: is this the right approach? If so, can
someone tell me how to start with a folded surface to generate the
Inflated, Ellipsoid surfaces, etc., that are normally generated during
the segmentation process in Caret? (e.g., the surfaces shown in Fig. 34
in the tutorial) I looked in the menus but couldn't find anything.
Thank you very much,
--Taosheng Liu
Taosheng,
I don't think there are any tutorials for doing what you want to do.
We had a tutorial for registering Freesurfer data, but it's pretty
outdated. We have scripts that are more helpful for that, and you may
end up adapting those.
It is possible to generate inflated, very inflated, ellipsoid, and
spherical surfaces using Surface: Geometry: Generate inflated (etc.)
from fiducial. Then in principle, you could use these inputs for
registration purposes.
In practice, we smooth the medial wall before registering our subjects,
which means drawing a border around it (or using auto-landmarks to do
so); smoothing just the encircled nodes; and then regenerating the
inflated, very inflated, and sphere using the fiducial with the
smoothed medial wall.
Depending on your purposes and how many subjects you have, you could
skip this step.
It used to be that you could draw borders only on 2D surfaces (i.e.,
flat). But now that you can draw on 3D surfaces, flattening can be
bypassed.
Have a look at the scripts described in this post:
http://www.mail-archive.com/[email protected]/msg01831.html
Even if you don't think you need scripts for your purpose, at least you
can see the steps we use to register Freesurfer-generated data, and if
there is something you don't understand, you can ask about it.
Donna
On 10/15/2009 09:12 AM, Taosheng Liu wrote:
Hello,
I'm new to Caret and I'd like to run spherical registration to the
atlas and do group analysis. Most of my analysis is done in custom
Matlab codes. I use a combination of FreeSurfer and SurfRelax (a less
used software) to do segmentation and surface recon.
I'm able to output my surface to Caret fomat, i.e., I can generate
topo and coords files for a folded hemisphere, and open/visualize them
in Caret. I tried to follow the Caret_5.5_Tutorial_Segment.pdf for
doing registration, but I'm currently stuck, because it seems to
require flattened/inflated/spherical surfaces of my subjects.
I'm imagining that I can start with my folded surface and do all
those things, and then follow the tutorial to do spherical
registration? My question for now is simply: is this the right
approach? If so, can someone tell me how to start with a folded surface
to generate the Inflated, Ellipsoid surfaces, etc., that are normally
generated during the segmentation process in Caret? (e.g., the surfaces
shown in Fig. 34 in the tutorial) I looked in the menus but couldn't
find anything.
Thank you very much,
--Taosheng Liu
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_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
--
Taosheng Liu
Assistant Professor
Department of Psychology
Michigan State University
East Lansing, MI 48824-1116
Ph: 517.432.6694
Fax: 517.353.1652
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