Hi Zuzana

1. the subcortical segmentations are based on the protocol defined by the Center for Morphometric Analysis at MGH, so you will need to look at their papers for e.g. hippocampus/amygdala segmentations

2. You should check with the CMA, but I believe it refers to cases with a cavum septum pellucidum.

3. The GCA is based on 40 manually labeled brain volumes, and the DK and Destrieux atlases are based on manually labeled surfaces.

4. The bankssts is a small region in the superior temporal sulcus where Ron Killiany found prominent AD effects. You should be able to find his paper on the topic with Marilyn Albert.

cheers Bruce

On Wed, 24 Jul 2013, Zuzana Nedelska wrote:

Hello,

I have attended short FSL/FreeSurfer course in New Zealand last year and have subscribed for mailing list, but in spite of all that I would I would appreciate very much to know.

1.)     1.)how GCA atlas that is used by FreeSurfer defines boundaries of subcortical volumes (especially amygdala and hippocampus). I  work in Mayo Clinic Center for Advanced Imaging Research now and I need to know these details (if possible) this for publication methods. We use and cite FreeSurfer often, but never went into details like this.

2.)    2.)What is ment by region of ‘5th ventricle’ in FS aseg.stats outputs and LUTs color coding table? From anatomical point of view, I am not sure what 5th ventricle is

3.)    3.)Do I correctly understand that subcortical segmentation is based on manually labeled GCA atlas, and cortical parcellation is based either on Desikan-Killiany atlas with 33 ROIS/hemisphere, or Destrieux atlas with 73 ROIs/hemisphere?

4.)    4.)What is cortical region named ‘bankssts’ in Desikan-Killiany atlas?

I would greatly appreciate your reply or suggestion where to find these information ASAP.

Thank you,

Zuzana Nedelska