Hey Bruce, Thank you for the informations. May I ask you few additional questions?
A) In your answer to my first question you wrote "you can also just look at the map itself without averaging over an ROI". What does this mean in reference to calculation of the cortical thickness. B) For my question B in my previous e mail, may be I was not clear, I am actually asking you about the information present in the ?.aparc .stats file that is not in the table. As I understand the table represents the different ROI and has information of the mean (average) thickness within each ROI of the cortical parcellation ( 35 different regions). But there are some additional information present before the table begins. And it says # Measure Cortex,NumVert,Number of Vertices, 143103, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 94823.1, mm^2 # Measure Cortex, MeanThickness,Mean Thickness, 2.62665, mm My question is about this measurement. What does this Cortical measure mean thickness is representing? C) Can you please explain me a little bit in detain how would I run the mris_anatomical_stats, I mean can you help me with the command line or suggest me a tutorial where I can find the information? D) I don't know what is qdec? Please advise. E) If I want to know the total cortical surface area do I add up the surface area measurements for each ROI given in the table for each hemisphere and then I add the two individual hemisphere measurements for getting the total cortical surface area? Looking forward for your response, Thanks, Rashmi. " On 1/18/12 9:18 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote: 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. 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