I loaded in lh.white and rh.white and the white and pial surfaces look fine, as does the aseg.mgz.

Thanks, Elias

On Tue, 2010-05-25 at 09:08 -0400, Bruce Fischl wrote:

Hi Elias,

have you looked at the surfaces? Are they correct?

Bruce On Mon, 24 May 2010, Elias Kersten wrote:

...

Hi,

I am trying to run a subject through the entire recon-all pipeline. However, I noticed the second to last step, "-wmparc", was taking a very long time (days).

Looking over the data, the aparc+aseg.mgz file is almost all labeled as "Left-Cerebral-White-Matter", including the background. Also, the lh.ribbon.mgz file appears like a series of speckles, while the rh.ribbon.mgz file looks normal.

I'm not sure where this problem is originating from or what my next steps should be. Any suggestions?

Thanks, Elias

---

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.

How does the aparc+aseg.mgz look?

Bruce Fischl wrote:

Not sure then. Krish: can you take a look?

On Tue, 25 May 2010, Elias Kersten wrote:

...

I loaded in lh.white and rh.white and the white and pial surfaces look fine, as does the aseg.mgz.

Thanks, Elias

On Tue, 2010-05-25 at 09:08 -0400, Bruce Fischl wrote:

...

Hi Elias,

have you looked at the surfaces? Are they correct?

Bruce On Mon, 24 May 2010, Elias Kersten wrote:

...

Hi,

I am trying to run a subject through the entire recon-all pipeline. However, I noticed the second to last step, "-wmparc", was taking a very long time (days).

Looking over the data, the aparc+aseg.mgz file is almost all labeled as "Left-Cerebral-White-Matter", including the background. Also, the lh.ribbon.mgz file appears like a series of speckles, while the rh.ribbon.mgz file looks normal.

I'm not sure where this problem is originating from or what my next steps should be. Any suggestions?

Thanks, Elias

---

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

And all the surfaces look ok? Try looking at them with

tkmedit subjectname orig.mgz -seg aseg.mgz -surfs

Elias Kersten wrote:

The subcortical structures, brainstem, thalamus, cerebellum appear to be labeled correctly, but the rest of the brain and background are labeled as Left-Cerebral-White-Matter.

On Tue, 2010-05-25 at 11:51 -0400, Douglas N Greve wrote:

...

How does the aparc+aseg.mgz look?

Bruce Fischl wrote:

...

Not sure then. Krish: can you take a look?

On Tue, 25 May 2010, Elias Kersten wrote:

...

I loaded in lh.white and rh.white and the white and pial surfaces look fine, as does the aseg.mgz.

Thanks, Elias

On Tue, 2010-05-25 at 09:08 -0400, Bruce Fischl wrote:

...

Hi Elias,

have you looked at the surfaces? Are they correct?

Bruce On Mon, 24 May 2010, Elias Kersten wrote:

...

Hi,

I am trying to run a subject through the entire recon-all pipeline. However, I noticed the second to last step, "-wmparc", was taking a very long time (days).

Looking over the data, the aparc+aseg.mgz file is almost all labeled as "Left-Cerebral-White-Matter", including the background. Also, the lh.ribbon.mgz file appears like a series of speckles, while the rh.ribbon.mgz file looks normal.

I'm not sure where this problem is originating from or what my next steps should be. Any suggestions?

Thanks, Elias

---

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

One additional note: I had previously processed this subject through FreeSurfer version 4.0.2 without any problems. For some reason this problem only occurred upon reprocessing with version 4.5.0. I batch processed this subject with about 50 others, and the other subjects look fine.

Any other suggestions?

Thanks, Elias

On Tue, 2010-05-25 at 14:25 -0500, Elias Kersten wrote:

I tried the recommended syntax below for looking at the surfaces and they look fine in all three views (coronal, horizontal and sagittal). And the surfaces seem consistent with other subjects I've processed.

Thanks, Elias

On Tue, 2010-05-25 at 14:40 -0400, Douglas N Greve wrote:

...

And all the surfaces look ok? Try looking at them with

tkmedit subjectname orig.mgz -seg aseg.mgz -surfs

Elias Kersten wrote:

...

The subcortical structures, brainstem, thalamus, cerebellum appear to be labeled correctly, but the rest of the brain and background are labeled as Left-Cerebral-White-Matter.

On Tue, 2010-05-25 at 11:51 -0400, Douglas N Greve wrote:

...

How does the aparc+aseg.mgz look?

Bruce Fischl wrote:

...

Not sure then. Krish: can you take a look?

On Tue, 25 May 2010, Elias Kersten wrote:

...

I loaded in lh.white and rh.white and the white and pial surfaces look fine, as does the aseg.mgz.

Thanks, Elias

On Tue, 2010-05-25 at 09:08 -0400, Bruce Fischl wrote:

> Hi Elias, > > have you looked at the surfaces? Are they correct? > > Bruce > On Mon, 24 May 2010, > Elias Kersten wrote: > > > >> Hi, >> >> I am trying to run a subject through the entire recon-all pipeline. >> However, I noticed the second to last step, "-wmparc", was taking a very >> long time (days). >> >> Looking over the data, the aparc+aseg.mgz file is almost all labeled as >> "Left-Cerebral-White-Matter", including the background. Also, the >> lh.ribbon.mgz file appears like a series of speckles, while the >> rh.ribbon.mgz file looks normal. >> >> I'm not sure where this problem is originating from or what my next >> steps should be. Any suggestions? >> >> Thanks, >> Elias >> >> >> _______________________________________________ >> 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

Hey Bruce,

I've uploaded the data via ftp to: transfer/incoming/EK_umn_052710.tar.gz

Please let me know if I can supply any further information. Thanks for taking a look!

-Elias

On Thu, 2010-05-27 at 10:58 -0400, Bruce Fischl wrote:

no idea. Can you tar and gzip the subject and put it on our filedrop?

thanks Bruce On Thu, 27 May 2010, Elias Kersten wrote:

...

One additional note: I had previously processed this subject through FreeSurfer version 4.0.2 without any problems. For some reason this problem only occurred upon reprocessing with version 4.5.0. I batch processed this subject with about 50 others, and the other subjects look fine.

Any other suggestions?

Thanks, Elias

On Tue, 2010-05-25 at 14:25 -0500, Elias Kersten wrote:

...

I tried the recommended syntax below for looking at the surfaces and they look fine in all three views (coronal, horizontal and sagittal). And the surfaces seem consistent with other subjects I've processed.

Thanks, Elias

On Tue, 2010-05-25 at 14:40 -0400, Douglas N Greve wrote:

...

And all the surfaces look ok? Try looking at them with

tkmedit subjectname orig.mgz -seg aseg.mgz -surfs

Elias Kersten wrote:

...

The subcortical structures, brainstem, thalamus, cerebellum appear to be labeled correctly, but the rest of the brain and background are labeled as Left-Cerebral-White-Matter.

On Tue, 2010-05-25 at 11:51 -0400, Douglas N Greve wrote:

...

How does the aparc+aseg.mgz look?

Bruce Fischl wrote:

> Not sure then. Krish: can you take a look? > > On Tue, 25 May 2010, Elias Kersten wrote: > > > >> I loaded in lh.white and rh.white and the white and pial surfaces look >> fine, as does the aseg.mgz. >> >> Thanks, >> Elias >> >> On Tue, 2010-05-25 at 09:08 -0400, Bruce Fischl wrote: >> >> >>> Hi Elias, >>> >>> have you looked at the surfaces? Are they correct? >>> >>> Bruce >>> On Mon, 24 May 2010, >>> Elias Kersten wrote: >>> >>> >>> >>>> Hi, >>>> >>>> I am trying to run a subject through the entire recon-all pipeline. >>>> However, I noticed the second to last step, "-wmparc", was taking a very >>>> long time (days). >>>> >>>> Looking over the data, the aparc+aseg.mgz file is almost all labeled as >>>> "Left-Cerebral-White-Matter", including the background. Also, the >>>> lh.ribbon.mgz file appears like a series of speckles, while the >>>> rh.ribbon.mgz file looks normal. >>>> >>>> I'm not sure where this problem is originating from or what my next >>>> steps should be. Any suggestions? >>>> >>>> Thanks, >>>> Elias >>>> >>>> >>>> _______________________________________________ >>>> 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 > > > >