Hello Bruce,

I am just checking in as I am curious if there has been any update available regarding the entorhinal and perirhinal annot/labelling? I hope I haven't missed anything.

Thank you!

Yi Leng

On Sun, Feb 10, 2019, 16:32 Yi Leng Fung <yfung@student.unimelb.edu.au> wrote:

Hello Bruce,

I have uploaded a tarred and gzipped subject onto the ftp site. Do let me know if there is anything else I could help with.

Cheers,
Yi Leng

On Sat, Feb 9, 2019 at 2:25 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Yi-Leng

can you upload the worst subject to our ftp site (the entire gzipped and
tarred subject dir please).

cheers
Bruce
On Fri, 8 Feb 2019, Yi Leng Fung wrote:

>
>         External Email - Use Caution
>
> [64b4f0f085b91c1f8130601d2cf65e8861fc5b7f.png?u=328927]
> Hello Bruce,
>
> On all four of our studies, the labels and the annot look similar in the sense that almost the entire
> rh.perirhinal_exvivo.thresh.label was contained within the rh.entorhinal_exvivo.thresh.label (screenshot of the
> right hemisphere with labels and annot attached for your reference). The resulting annot label shows an extremely
> under-represented perirhinal on the right hemispheres. The left hemispheres did not show such a dramatic overlap.
>
> Cheers,
> Yi-Leng
>
>
> On Fri, Feb 8, 2019 at 3:44 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> Do the labels look better than the annot?
>
> On Feb 6, 2019, at 10:15 PM, Yi Leng Fung <yfung@student.unimelb.edu.au> wrote:
>
>          External Email - Use Caution
>
> Hello FreeSurfer team,
>
> Thank you for providing the recon-all patch. We have applied this to four studies and have seen a
> notable difference between in the representation of entorhinal over perirhinal on the right hemisphere
> labelling on each analysis ran. The left hemisphere appears to have less overlap.
>
> I have attached a screenshot of both hemispheres to demonstrate. Would really appreciate any feedback.
> Thanks!
>
> Cheers,
> Yi-Leng
>
>
> 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
>
> Image removed by sender.
>
> 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
> > > > >
> > > > >
> > > > >_______________________________________________
> > > > 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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> <screenshot_20190207_rh_perirhinal_obscured_recon-all_patch.png>
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