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 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/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe

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 mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto: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 development version at ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/ ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/ ).

Here is the image again:

<unknown.png> Kind regards, Bronwyn Overs Research Assistant

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/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe

...

On 6 Mar 2017, at 1:17 pm, Bronwyn Overs <b.overs@neura.edu.au mailto: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 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/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailto: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.

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 development versionat ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/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.

Hi Bruce,

Just wanted to check in and see if you had examined the files I uploaded yet? Kind regards, Bronwyn Overs Research Assistant

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/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe

On 16 May 2017, at 10:27 am, 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 mailto:fischl@nmr.mgh.harvard.edu). Please let me know if you require any additional information. Kind regards, Bronwyn Overs Research Assistant

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/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe

...

On 5 May 2017, at 8:25 am, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto: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 <mailto: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 http://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 <mailto: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 mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto: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 development versionat ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cento ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/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 http://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 <mailto: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 http://neura.edu.au/ Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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.

Hi Bruce,

Sure, files have been dropped again. Kind regards, Bronwyn Overs Research Assistant

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/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe

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 mailto: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 mailto:fischl@nmr.mgh.harvard.edu). Please let me know if you require any additional information. Kind regards, Bronwyn Overs Research Assistant

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/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe

...

On 5 May 2017, at 8:25 am, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto: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 <mailto: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 http://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 <mailto: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 mailto: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 mailto:freesurfer@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto: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 development versionat ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cento ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/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 http://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 <mailto: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 http://neura.edu.au/ Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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.

---

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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 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.

Hi Bruce,

That's fine, thanks very much.

Bronwyn Overs

Research Assistant

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

[ http://neura.edu.au/ | neura.edu.au  ]

[ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | 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 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.

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/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.

---

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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. _______________________________________________ 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.

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

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
  >       _______________________________________________
  >       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.
  _______________________________________________
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  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
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  HelpLine at
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  sent to you
  in error
  but does not contain patient information, please contact
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  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.

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.edumailto: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.auhttp://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 > _______________________________________________ > 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. _______________________________________________ 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.edumailto: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.

Sure thing, just let me know the filename once it's uploaded. 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: Wednesday, August 02, 2017 10:02 PM To: Freesurfer support list Subject: Re: [Freesurfer] Medial Surface Problem

Hi Andrew,

Thanks for taking a look at the files and for this feedback.

I have also spoken to a colleague of mine who was also experiencing the same medial surface problem with his scans (Yann Quidé). However, he was using the standard version 5.3 installation of freesurfer without the updated mris_make_surfaces binary. He is going to upload those file today via your FTP site. It would be great if you can confirm if the source of the problem Yann is having is the same as our medial surface problem, or if our problem really is caused by using the updated binary with the original freesurfer installation.

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 29 Jul 2017, at 7:03 am, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bronwyn Overs <b.overs@neura.edu.aumailto: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.auhttp://neura.edu.au/ <http://neura.edu.auhttp://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.edumailto:fischl@nmr.mgh.harvard.edumailto: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.auhttp://neura.edu.au/<http://neura.edu.auhttp://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.edumailto: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.auhttp://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.aumailto: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.auhttp://neura.edu.au/ Twitter | Facebook | Subscribe ___________________________________________________________________________ _ From: "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto: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.auhttp://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.edumailto: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.aumailto: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.edumailto: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.auhttp://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.edumailto: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.aumailto: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.auhttp://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.commailto: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.aumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.auhttp://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.aumailto: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.auhttp://neura.edu.au/ Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

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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.edumailto: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.edumailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edumailto: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.

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