Hello Bruce,

Thank you very much for your quick response.

I do have another point of confusion regarding the BA.thresh.annot file. When visualised in Freeview (using Bert as the example), the BA.thresh annotation file labelled the medially located structure as the perirhinal cortex and the laterally located structure as the entorhinal cortex.

I find that quite puzzling as I understand their relative anatomical location to be the reverse; I would really appreciate it if you could clarify why it is labelled as such in the annot file?

Again, thank you for your time in helping me understand this.

Cheers,

Yi-Leng

On Tue, Feb 5, 2019, 04:26 Bruce Fischl <fischl@nmr.mgh.harvard.edu wrote:

Hi Yi-Leng

the annot file contains the label with the max p-value at each location.
The thresholded .label files are computed to have the surface area that
matches the average of the training labels, so they will not be the same.

cheers
Bruce

On
Tue, 5 Feb 2019, Yi Leng Fung wrote:

>
> External Email - Use Caution
>
> Dear FreeSurfer Developers,
>
> Prior to extracting the gray volume numbers of the entorhinal and perirhinal cortex from
> ?h.BA_exvivo.thresh.stats file, I was examining the entorhinal and perirhinal cortex on the
> ?h.BA.thresh.annot on Freeview. However, I noted that their locations on the annot file did not
> correspond to the (non-overlapping) locations indicated by ?h.entorhinal.thresh.label and
> ?h.perirhinal.thresh.label.
>
> I have also loaded the annot files and label files from the fully recon-ed subject named "bert" on
> Freeview and observed the same mismatch in the labeling. I am curious why this might be the case.
>
> I have searched the archive and have not been able to find any similar queries on this, hence it would be
> of tremendous help if someone could clarify this observation. If it is of interest, I am running
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 on Ubuntu 16.04.
>
> Thank you for your assistance and I look forward to hearing from you.
>
> Best regards,
> Yi-Leng
>
>
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