On Wed, Feb 6, 2019 at 3:11 AM Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

Hi Yi Leng, there’s a recon-all patch for 6.0 at https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all. You can update it with:

cd ${FREESURFER_HOME}/bin

mv recon-all recon-all.backup

curl https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all -o recon-all

chmod +x recon-all

Let us know if that works!

thanks

Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yi Leng Fung <yfung@student.unimelb.edu.au>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, February 4, 2019 at 9:17 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: Jean Augustinack <jean@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label

        External Email - Use Caution

Thank you!

Cheers,

Yi Leng

On Tue, Feb 5, 2019 at 1:05 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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 <fischl@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 <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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> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
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> >
> >
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