thanks. It is almost certainly a bug in recon-all. I'm testing a fix
tomorrow and hopefully we can have one out to you (and the rest of the
list) by tomorrow.
Sorry!
Bruce
On Tue, 5 Feb 2019, Yi Leng Fung wrote:
External Email - Use Caution
[3a1715320c6fbab489126e656ad6e765d6e0a6ee.png?u=328927]
Hello Bruce,
Yep, the exvivo entorhinal thresh label overlay on the perirhinal annotation. I
have attached a screenshot of it
for your reference.
Cheers,
Yi-Leng
On Tue, Feb 5, 2019 at 12:31 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
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
<fis...@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
<fis...@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
> > >
> > >
> > >_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >_______________________________________________
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>
>
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