Recon all takes the vertices ....and assigns them to a parcel using the gcs atlases ... these labelings are the annot files and they are used to generate the autoparcellated pial surfaces

Because there are 3 atlases in the recon all pipeline... three parcellations are made and they are named accordingly

Aparc plus aseg takes the cortical parcellation file and combines it with the segmentation aseg... thus aparc+aseg is a labeling of the cortex and subcortex with each of the three cortical parcellation schemes

On 9 Jan. 2019 1:12 pm, "Yerong Li" <yerong.li@rice.edu> wrote:

External Email - Use Caution

Dear Freesurfer experts:

I am on ROI analysis tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0

And I am trying to understand the relationship between:

/label/?h.aparc.annot and /mri/aparc+aseg.mgz
/label/?h.aparc.a2009s.annot and /mri/aparc.a2009s+aseg.mgz

I understand /label/?h.aparc.annot corresponds to "Desikan-Killiany
atlas" and its labels have 35 different labels (except unknown 0),
while in several cases you mentioned that "/mri/aparc+aseg.mgz"
corresponds to "Desikan-Killiany atlas", which I DO NOT understand.
"/mri/aparc+aseg.mgz" to me are subcortical segmentations while
"/label/?h.aparc.annot" are cortical(surface) parcellations.
"Desikan-Killiany atlas" should mean "cortical (surface)
parcellations". That's why I do not understand why
"/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas"?

Could anyone help me understand this?

Yerong

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