Hello, I have uploaded the subject/mri/orig/001.mgz file for the participant with the error described here:

https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/22563/1/7580a7af...

Thanks, Jennifer

On Mon, Nov 29, 2010 at 7:55 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Jennifer,

if you put this on our drop site we'll take a look.

cheers Bruce

On Mon, 29 Nov 2010, Jennifer Addicks wrote:

...

Hello,

I have completed cortical reconstructions for 79 of 80 scans without error. However, the recon for one participant exited during topology correction with the following error message:

ERROR: _FindFacePath: could not find path! Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

recon-all exited with ERRORS at Sun Nov 28 19:32:14 EST 2010

This error has been posted to the archive previously but the solution does not seem to accompany it. Any help would be appreciated.

Thanks, Jennifer _______________________________________________ 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.

Hello,

I'm facing the same problem for one of my subjects. Is there a general solution for this problem or would you solve this problem on a case by case basis? I saw posts from others with the same problem.

Thanks for your help, Nasim On Nov 29, 2010, at 7:55 AM, Bruce Fischl wrote:

Hi Jennifer,

if you put this on our drop site we'll take a look.

cheers Bruce

On Mon, 29 Nov 2010, Jennifer Addicks wrote:

...

Hello,

I have completed cortical reconstructions for 79 of 80 scans without error. However, the recon for one participant exited during topology correction with the following error message:

ERROR: _FindFacePath: could not find path! Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

recon-all exited with ERRORS at Sun Nov 28 19:32:14 EST 2010

This error has been posted to the archive previously but the solution does not seem to accompany it. Any help would be appreciated.

Thanks, Jennifer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

what does "old topo fixer" mean? thanks ilana

On 15 February 2011 09:55, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Nasim,

can you tar and gzip the entire subject dir and send it to us? I'll try to track it down. In the mean time if you just rerun with the old topo fixer it should work. Nick can post the appropriate flags

cheers Bruce On Tue, 15 Feb 2011, Nasim Maleki wrote:

...

Hello,

I'm facing the same problem for one of my subjects. Is there a general

solution for this problem or would you solve this problem on a case by case basis? I saw posts from others with the same problem.

...

Thanks for your help, Nasim On Nov 29, 2010, at 7:55 AM, Bruce Fischl wrote:

...

Hi Jennifer,

if you put this on our drop site we'll take a look.

cheers Bruce

On Mon, 29 Nov 2010, Jennifer Addicks wrote:

...

Hello,

I have completed cortical reconstructions for 79 of 80 scans without error. However, the recon for one participant exited during topology correction with the following error message:

ERROR: _FindFacePath: could not find path! Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

recon-all exited with ERRORS at Sun Nov 28 19:32:14 EST 2010

This error has been posted to the archive previously but the solution does not seem to accompany it. Any help would be appreciated.

Thanks, Jennifer _______________________________________________ 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

---

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 Ilana,

Nick kindly helped me addressing this issue in one of my subjects. In my case the brainmask had some cortex stripped from the top and the failure had stemmed from there. I would suggest that you also check your brainmask.mgz and see if the skull stripping was successful there. If that is the case you can correct it by adjusting the watershed value (increase it). Please check this link:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial

Nasim On Feb 18, 2011, at 3:34 PM, Ilana Hairston wrote:

what does "old topo fixer" mean? thanks ilana

On 15 February 2011 09:55, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nasim,

can you tar and gzip the entire subject dir and send it to us? I'll try to track it down. In the mean time if you just rerun with the old topo fixer it should work. Nick can post the appropriate flags

cheers Bruce On Tue, 15 Feb 2011, Nasim Maleki wrote:

...

Hello,

I'm facing the same problem for one of my subjects. Is there a general solution for this problem or would you solve this problem on a case by case basis? I saw posts from others with the same problem.

Thanks for your help, Nasim On Nov 29, 2010, at 7:55 AM, Bruce Fischl wrote:

...

Hi Jennifer,

if you put this on our drop site we'll take a look.

cheers Bruce

On Mon, 29 Nov 2010, Jennifer Addicks wrote:

...

Hello,

I have completed cortical reconstructions for 79 of 80 scans without error. However, the recon for one participant exited during topology correction with the following error message:

ERROR: _FindFacePath: could not find path! Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

recon-all exited with ERRORS at Sun Nov 28 19:32:14 EST 2010

This error has been posted to the archive previously but the solution does not seem to accompany it. Any help would be appreciated.

Thanks, Jennifer _______________________________________________ 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

---

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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peligro! flaca pero mala!

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