Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883
Hi Bruce,
That's fine, thanks very much.
Bronwyn Overs
Research Assistant
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
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
> the developmentversionat ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/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
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended
> only for
> the person to whom it is
> addressed. If you believe this e-mail was sent
> to
> you in error and the e-mail
> contains patient information, please contact
> the
> Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If
> the
> e-mail was sent to you in error
> but does not contain patient information,
> please
> contact the sender and properly
> dispose of the e-mail.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended
> only for the
> person to whom it is
> addressed. If you believe this e-mail was sent
> to you in
> error and the e-mail
> contains patient information, please contact
> the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If
> the e-mail was
> sent to you in error
> but does not contain patient information,
> please contact
> the sender and properly
> dispose of the e-mail.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended
> only for the person
> to whom it is
> addressed. If you believe this e-mail was sent
> to you in error
> and the e-mail
> contains patient information, please contact
> the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If
> the e-mail was sent
> to you in error
> but does not contain patient information,
> please contact the
> sender and properly
> dispose of the e-mail.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended
> only for the person to whom
> it is
> addressed. If you believe this e-mail was sent
> to you in error and the
> e-mail
> contains patient information, please contact
> the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If
> the e-mail was sent to you
> in error
> but does not contain patient information,
> please contact the sender
> and properly
> dispose of the e-mail.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the
> person to whom it is
> addressed. If you believe this e-mail was sent to you in
> error and the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was
> sent to you in error
> but does not contain patient information, please contact
> the sender and properly
> dispose of the e-mail.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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
> the developmentversionat ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/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
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended
> only for
> the person to whom it is
> addressed. If you believe this e-mail was sent
> to
> you in error and the e-mail
> contains patient information, please contact
> the
> Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If
> the
> e-mail was sent to you in error
> but does not contain patient information,
> please
> contact the sender and properly
> dispose of the e-mail.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended
> only for the
> person to whom it is
> addressed. If you believe this e-mail was sent
> to you in
> error and the e-mail
> contains patient information, please contact
> the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If
> the e-mail was
> sent to you in error
> but does not contain patient information,
> please contact
> the sender and properly
> dispose of the e-mail.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended
> only for the person
> to whom it is
> addressed. If you believe this e-mail was sent
> to you in error
> and the e-mail
> contains patient information, please contact
> the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If
> the e-mail was sent
> to you in error
> but does not contain patient information,
> please contact the
> sender and properly
> dispose of the e-mail.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended
> only for the person to whom
> it is
> addressed. If you believe this e-mail was sent
> to you in error and the
> contains patient information, please contact
> the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If
> the e-mail was sent to you
> in error
> but does not contain patient information,
> please contact the sender
> and properly
> dispose of the e-mail.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the
> person to whom it is
> addressed. If you believe this e-mail was sent to you in
> error and the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was
> sent to you in error
> but does not contain patient information, please contact
> the sender and properly
> dispose of the e-mail.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.