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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