On Wed, 18 Jan 2012, Rashmi Singh wrote:
Hello,
This is Rashmi. I am very new to neurobiology and computing and my very
first project involves measuring cortical thickness from the reconstructed
surfaces generated by FreeSurfer. I have recently started to self teach
myself FreeSurfer, but with a background in immunology and almost no
background in neurobiology I know I have a long way to go and need a lot of
help.
I have learnt to run FreeSurfer and am currently using Version 5.1.0. I am
also referring the FreeSurfer Lectures and Tutorial available online for
free to learn usage of Tktools. Despite that I don't have access to your
tutorial data, I have found this tutorial helpful in learning how to use
Tktools to view volumes and surfaces.
At present I have few basic (naïve) questions that I need your help with,
excuse me if you find my question ignorant.
A)My first question is about the cortical parcellation stats files.
After running the recon all on my MPRAGE data, I did get the ?.aparc.stats
file in the stats folder. I also see ?.aparc.a2009S.stats files. I read and
kind of understood the difference between these two files in how differently
they calculate the gray matter.
My question is which of these two files should be considered for measurement
as generated by the automated calculation of the cortical thickness.
the thickness is a map over the whole cortex. The aparc and aparc.a2009S
are different regions of interest (ROIs) that follow different anatomical
conventions. You can use either to obtain the average thickness in the ROIs
contained in each, but you can also just look at the map itself without
averaging over an ROI.
B) Besides the cortical thickness parameters the ?.aparc file has
information on the white surface area and the mean thickness.
Is the mean thickens represents the average cortical thickness of the
respective hemisphere? If not what does it represents and how can
I calculate the hemisphere based cortical thickness?
the mean thickness is the mean within each ROI. mris_anatomical_stats will
compute the mean thickness over the hemi if you want.
C) How would I calculate the average cortical thickness of the whole brain?
average the two hemi thicknesses. That will be close enough
D) In research articles related to measurement of cortical thickness,
authors have reported mapping of the thickness measured on the inflated or
semi-inflated surface . How is it done and what is the significance of doing
it.
this is for visualization. Just bring up the inflated surface in tksurfer
and load the lh or rh thickness.
E)Once I have the measure of all the cortical thickness how do I compare all
the Subjects measurements participating in my study?
qdec is probably the easiest way to do this.
F) Do you in your tutorial have some reference images for labelled
subcortical regions that are generated in aseg.mgz files.
yes, we use an atlas that we compiled from manually labeled subjects here
at MGH.
Thanks for your response in advance.
Hope to hear from you soon.
Regards,
Rashm.
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