Dear Reetta-Liina, Thanks for pointing out this inconsistency. The mapping is: GC-ML-DG = GC-DG CA3 = CA2/3 molecular_layer_HP = molecular layer Cheers, /Eugenio

Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 7 Mar 2017, at 19:41, Reetta-Liina Säilä <rlsail@utu.fimailto:rlsail@utu.fi> wrote:

Hello All,

I have done the hippocampus segmentation with dev version 6 (Downloaded on 26th March 2016).

I have difficulties in determing what the output labels consist of.

The outputfile names are these: left_Hippocampal_tail left_subiculum left_CA1 left_hippocampal-fissure left_presubiculum left_parasubiculum left_molecular_layer_HP left_GC-ML-DG left_CA3 left_CA4 left_fimbria left_HATA left_Whole_hippocampus (and the same on the right side)

But, there are some discrepancies between these output labels and Eugenio Iglesias' article (attached). First, more often I see GC-ML-DG labeled as GC-DG, what is the difference between these two? Is the dentate gyrus' molecular layer included in GC-ML-DG / GC-DG or not?

In summary, my question is: what structures exactly are included in the labels of dev version 6: - GC-ML-DG - molecular_layer_HP -CA3 And which labels correspond these on the final version of Freesurfer 6?

These are the discrepancies on the article attached on pages 2, and 7.

1) The article says on page 2: - The T2 images are often acquired anisotropically, such that resolution along the direction of the major axis of the hippocampus is reduced in exchange for higher in-plane resolution within each coronal slice. This design choice is motivated by the internal structure of the hippocampus: resembling a Swiss roll, its spiral structure changes less rapidly along its major axis, which is almost parallel to the anterior-posterior direction. In in vivo T2-weighted data, part of this spiral becomes visible as a hypointense band that corresponds to the stratum radiatum, lacunosum moleculare, hippocampal sulcus and molecular layer of the dentate gyrus. These layers separate the hippocampus from the dentate gyrus. Henceforth, for simplicity in writing, we will refer to this band as the “molecular layer”.

2) On page 7: "Molecular layer: This label consists of two parts, molecular layer for subiculum or molecular layer for CA fields. The molecular layer appears as dark contrast that lies directly underneath the hippocampal fissure and above the subiculum. The molecular layer of the hippocampus continues as dark contrast that forms between the CA regions and the GC-DG as well as the hippocampal fissure. The molecular layer follows the shape of the hippocampal folds."

I am little confused of this 'molecular layer' term in the previous contexts, and what the actual output label 'molecular layer' consists of.

Has someone gone through this already?

Thank you!

Best, Reetta-Liina <subfieldsNeuroimage2015preprint.pdf>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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