Hi Yi-Leng

eek! Can you verify that the lh.entorhinal_exvivo.thresh.label is
correct? Does it overlay on the perirhinal annotation?

thanks
Bruce

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

>
>         External Email - Use Caution        
>
> [3f1a37b0d4514e4a90a5d3340afcefe6c789830e.png?u=328927]
> Hello All,
>
> Here it is, both are from bert. 
>
> Thank you for looking into this.
>
> Cheers,
> Yi-Leng
>
> On Tue, Feb 5, 2019 at 7:47 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       Hi Yi-Leng
>
>       can you send us an image of the parcellaton on an inflated surface so we
>       can see?
>
>       thanks
>       Bruce
>
>
>       On Tue, 5 Feb 2019, Yi Leng Fung wrote:
>
>       >
>       >         External Email - Use Caution        
>       >
>       > 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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