On 29 Jul 2017, at 7:03 am, Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

Hi Bronwyn, I tried to replicate your issue using both v5.3 and the current dev environment, but I had no luck. I'm guessing the problem has to do with combining the development binary along with 5.3, so I suggest using the 5.3 version of mris_make_surfaces to fix this.

best,
Andrew
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bronwyn Overs <b.overs@neura.edu.au>
Sent: Sunday, July 09, 2017 7:32 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Medial Surface Problem

Hi Bruce,

I have now re-uploaded all the requested files and info via the ftp site (see below). The zipped file name is fsMedialSurfaceProblem.zip

Name (surfer.nmr.mgh.harvard.edu:Bronwyn): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put fsMedialSurfaceProblem.zip
local: fsMedialSurfaceProblem.zip remote: fsMedialSurfaceProblem.zip
229 Entering Extended Passive Mode (|||37889|).
150 Ok to send data.
100% |***********************************|  2017 MiB   51.01 KiB/s    00:00 ETA
226 Transfer complete.
2116019235 bytes sent in 11:15:08 (51.01 KiB/s)


Kind regards,

Bronwyn Overs
Research Assistant

[Neuroscience Research Australia]

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

[Follow @neuraustralia on twitter]<https://twitter.com/neuraustralia>[Follow NeuRA on facebook]<https://www.facebook.com/NeuroscienceResearchAustralia>[Subscribe to the NeuRA Magazine]<http://www.neura.edu.au/help-research/subscribe>

On 5 Jul 2017, at 3:40 am, Bruce Fischl <fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> wrote:

sure. Can you upload the data again to our ftp site? Don't use the filedrop - use ftp and make sure you include the cross and the long of all the timepoints for this subject, and also the coordinates of the location you are seeing the problem


cheers
Bruce


On Tue, 4 Jul 2017, Bronwyn Overs wrote:

Thanks Bruce.
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au<http://neura.edu.au>
Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the
NeuRA Magazine

    On 3 Jul 2017, at 11:55 pm, Bruce Fischl
    <fischl@nmr.mgh.harvard.edu> wrote:
Hi Bronwyn
not yet, but we'll get to it soon
cheers
Bruce
On Mon, 3 Jul 2017, Bronwyn Overs wrote:

    Hi Bruce,
    Just wanted to check in on the status of reviewing our
    medial surface
    problem. Any luck so far?
    Kind regards,
    Bronwyn Overs
    Research Assistant
    Neuroscience Research Australia
    Neuroscience Research Australia
    Margarete Ainsworth Building
    Barker Street Randwick Sydney NSW 2031 Australia
    M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
    neura.edu.au
    Follow @neuraustralia on twitter Follow NeuRA on facebook
    Subscribe to the
    NeuRA Magazine

         On 14 Jun 2017, at 9:52 am, Bronwyn Overs
    <b.overs@neura.edu.au>
         wrote:
    Hi Bruce,
    That's fine, thanks very much.
    Bronwyn Overs
    Research Assistant
    <neura-logo-email.png>
    Neuroscience Research Australia
    Margarete Ainsworth Building
    Barker Street Randwick Sydney NSW 2031 Australia
    M 0411 308 769 T +61 2 9399 1883
    neura.edu.au
    Twitter | Facebook | Subscribe
___________________________________________________________________________
    _
    From: "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
    To: "Freesurfer support list"
    <freesurfer@nmr.mgh.harvard.edu>
    Sent: Wednesday, 14 June, 2017 00:02:04
    Subject: Re: [Freesurfer] Medial Surface Problem
    thanks Bronwyn
    I got them. It will take a bit for us to get to as this is
    in the long
    stream and we have a new postdoc who will be taking it
    over.
    cheers
    Bruce
    On Tue, 13 Jun
    2017, Bronwyn Overs wrote:

Hi Bruce,
Sure, files have been dropped again.

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au

Follow @neuraustralia on twitter Follow NeuRA on

    facebook Subscribe
    to the

NeuRA Magazine


     On 13 Jun 2017, at 11:44 am, Bruce Fischl
     <fischl@nmr.mgh.harvard.edu> wrote:

Hi Bronwyn
Can you filedrop it again? I don't think I have it
Thanks
Bruce

On May 15, 2017, at 8:27 PM, Bronwyn Overs

    <b.overs@neura.edu.au>

wrote:

     Hi Bruce,
Thank you for offering to take a look at this medial

    surface

problem.

I have uploaded all of the relevant files to through the
Martinos Centre FileDrop v2.0 to your email address
(fischl@nmr.mgh.harvard.edu). Please let me know if you

    require

any additional information.

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au

Follow @neuraustralia on twitter Follow NeuRA on

    facebook

Subscribe to the NeuRA Magazine


     On 5 May 2017, at 8:25 am, Bruce Fischl
     <fischl@nmr.mgh.harvard.edu> wrote:

if someone can upload a dataset as well as the exact
coordinates of the problem I'll take a look

cheers
Bruce

On Fri, 5 May 2017, Yann Quidé wrote:

     Hi all,
     We also have the same issue, any
     idea/suggestion?
     Thanks.
     Yann

          On 27 Apr 2017, at 9:43 am, Bronwyn Overs
     <b.overs@neura.edu.au>
          wrote:
     Hi Mailing List,
     Still trying to solve the below medial surface
     problem. Does anyone
     have any ideas?
     Kind regards,
     Bronwyn Overs
     Research Assistant
     Neuroscience Research Australia
     Neuroscience Research Australia
     Margarete Ainsworth Building
     Barker Street Randwick Sydney NSW 2031
     Australia
     M 0411 308 769 T +61 2 9399 1883 F +61 2 9399
     1265
     neura.edu.au
     Follow @neuraustralia on twitter Follow NeuRA
     on facebook Subscribe to
     the NeuRA Magazine

          On 28 Mar 2017, at 10:51 pm, Yann Quidé
          <yannquide@gmail.com> wrote:
     Dear all,
     I have an equivalent issue with my data. Any
     idea on how to fix
     this?
     Thanks.
     Yann

          Begin forwarded message:
     From: Bronwyn Overs <b.overs@neura.edu.au>
     Subject: Re: [Freesurfer] Medial Surface
     Problem
     Date: 20 March 2017 10:28:37 am AEDT
     To: Freesurfer support list
     <freesurfer@nmr.mgh.harvard.edu>
     Reply-To: Freesurfer support list
     <freesurfer@nmr.mgh.harvard.edu>
     Hello again mailing list,
     Can anyone address the possible cause of the
     medial
     surface problem shown below (overestimating of
     rh medial
     surface, shows up in the long image and not
     the tp or base
     images). Forgot to mention that I am using
     freesurfer v5.3
     with an updated mris_make_surfaces binary
     (sourced from
    thedevelopmentversionat ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurf

    er/
    dev_binarie

     s/cento
     s6_x86_64/ ).
     Here is the image again:
     <unknown.png>
     Kind regards,
     Bronwyn Overs
     Research Assistant
     Neuroscience Research Australia
     Neuroscience Research Australia
     Margarete Ainsworth Building
     Barker Street Randwick Sydney NSW 2031
     Australia
     M 0411 308 769 T +61 2 9399 1883 F +61 2 9399
     1265
     neura.edu.au
     Follow @neuraustralia on twitter Follow NeuRA
     on facebook
     Subscribe to the NeuRA Magazine

          On 6 Mar 2017, at 1:17 pm, Bronwyn Overs
          <b.overs@neura.edu.au> wrote:
     Hi mailing list,
     I am currently processing a longitudinal image
     and
     have come across a problem at the medial
     surface in
     the long image (step 3). As you can see in the
     attached image, the rh medial surface has been
     significantly overestimated and extends into
     the lh
     surface. This error showed up only in only 1
     of the
     2 long images for this subject, and both the
     time-point images and the base are perfectly
     fine.
     Do you know why this is happening?
     <Screen Shot 2017-03-06 at 1.09.53 pm.png>
     Kind regards,
     Bronwyn Overs
     Research Assistant
     Neuroscience Research Australia
     Neuroscience Research Australia
     Margarete Ainsworth Building
     Barker Street Randwick Sydney NSW 2031
     Australia
     M 0411 308 769 T +61 2 9399 1883 F +61 2 9399
     1265
     neura.edu.au
     Follow @neuraustralia on twitter Follow NeuRA
     on
     facebook Subscribe to the NeuRA Magazine
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