Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label

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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:

...

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[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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  >       >

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...

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  >

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