[MINC-users] talairach transform

[Akemi Tomoda]

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Hello list,

Please bear with me for such rudimentary questions.

During these couple of months, I have been trying to deal with the
FreeSurfer study to measure the brain cortex morphometricaly. However, I am
having trouble with automatic cutting planes so need to know more about the
Talairach transform since I have 2 major reasons.

1) 60% of our samples failed at the end of stage one because FS could not
find a cutting plane. I'm still in the process of investigating this
As far as I know, the optimized sample (bert) data has the seed point being
chosen well, but I should manually select a seed point.

2) There is a significant difference between succeeded and unsucceeded
groups (P<0.05). The brain size of succeeded group (n=5); 1662.78+31.98 cm3,
on the other hand, the brain size of unsucceeded group (n=7); 1433.15+191.26
cm3. So I guess, the skull size, rather to say, the brain size should be
investigated more precisely, since I am dealing with pediatric samples.

Assuming the talairach is good, the manual gives a procedure for defining
the cutting planes.  I am used to running all the processing from the
command line using recon-all.  Is there a way to set the callosum point and
pontine point and still use the command line, or do I have to use the GUI in
if I want to do a manual cut?

Please let me know your idea at your earliest convenience.

In addition, I also would like to get hold of Dave MacDonalds surface
extraction stuff from the MNI. Please let me know how I can contact with
them.


With warmest personal regards,

Akemi Tomoda

Developmental Biopsychiatry Research Program
McLean Hospital of Harvard Medical School
atomoda@mclean.harvard.edu



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