Hi Sita,

Running it with the -no-wsgcaatlas seems to do the trick as far as avoiding a segmentation fault. The T1 looks like it has a some motion artifact--might that be causing problems? I checked the Talairach transform and it looks generally alright, although I think it could be improved with some tweaking. It passed the automatic failure detection each time I ran recon-all, though. Would you recommend trying to improve the transform so that things down the line run more smoothly?

Best, Mike

On Thu, Mar 18, 2010 at 1:22 PM, Sita Kakunoori sita@nmr.mgh.harvard.eduwrote:

Hi Mike,

Did you check the talairach. And how do nu.mgz and T1.mgz look. Also you could probably try running the following command to see if the skull strip step finishes without errors.

recon-all -skullstrip -no-wsgcaatlas -s <subjid>

Sita.

On Thu, 18 Mar 2010, Michael Waskom wrote:

Hi Bruce, Nick,

...

I'm getting a segmentation fault that's crashing recon-all at the start of the watershed during skull-stripping. I've tried this three times, once starting the unpacking stream fresh from the raw dicoms, and it keeps happening at exactly the same place. I've been reconstructing brains of other subjects in the same directory all the while, so I don't think it's a permissions issue of any sort.

Full recon-all log is atatched, but here's the section where it crashes:

*************************WATERSHED************************** Sorting... first estimation of the COG coord: x=116 y=166 z=95 r=51 first estimation of the main basin volume: 585576 voxelsSegmentation fault Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010

And here's the OS data from the bugr script:

FREESURFER_HOME: /software/Freesurfer/4.4.0

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0

Debian version: squeeze/sid

Kernel info: Linux 2.6.31-20-generic x86_64

Do you have any idea what might be going wrong?

Thanks! Mike

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 Sita, all,

I got the rest of the recon to run, made pial edits on the brainmask after autorecon2, and then reran it to the end. It looks like the reconstruction of the cortical surfaces and the inflation worked fine, but the cortical parcellation is totally scrambled. I'm attatching an image of the inflated left hemisphere with the aparc annotation overlay. (It looks much the same on the right hemisphere). I'm also attaching the recon-all.log file. Do you have any idea what might be causing this problem?

Thanks, Mike

On Thu, Mar 18, 2010 at 2:54 PM, Sita Kakunoori sita@nmr.mgh.harvard.eduwrote:

Hi Mike,

I don't think the motion artifact could've been causing this error. It's probably a good idea to fix the talairach if you think it's off because if you are reporting the talairach coordinates, you would want the talairach transform to be reasonably accurate.

Sita.

On Thu, 18 Mar 2010, Michael Waskom wrote:

Hi Sita,

...

Running it with the -no-wsgcaatlas seems to do the trick as far as avoiding a segmentation fault. The T1 looks like it has a some motion artifact--might that be causing problems? I checked the Talairach transform and it looks generally alright, although I think it could be improved with some tweaking. It passed the automatic failure detection each time I ran recon-all, though. Would you recommend trying to improve the transform so that things down the line run more smoothly?

Best, Mike

On Thu, Mar 18, 2010 at 1:22 PM, Sita Kakunoori <sita@nmr.mgh.harvard.edu

...

wrote:

...

Hi Mike,

Did you check the talairach. And how do nu.mgz and T1.mgz look. Also you could probably try running the following command to see if the skull strip step finishes without errors.

recon-all -skullstrip -no-wsgcaatlas -s <subjid>

Sita.

On Thu, 18 Mar 2010, Michael Waskom wrote:

Hi Bruce, Nick,

...

I'm getting a segmentation fault that's crashing recon-all at the start of the watershed during skull-stripping. I've tried this three times, once starting the unpacking stream fresh from the raw dicoms, and it keeps happening at exactly the same place. I've been reconstructing brains of other subjects in the same directory all the while, so I don't think it's a permissions issue of any sort.

Full recon-all log is atatched, but here's the section where it crashes:

*************************WATERSHED************************** Sorting... first estimation of the COG coord: x=116 y=166 z=95 r=51 first estimation of the main basin volume: 585576 voxelsSegmentation fault Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010

And here's the OS data from the bugr script:

FREESURFER_HOME: /software/Freesurfer/4.4.0

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0

Debian version: squeeze/sid

Kernel info: Linux 2.6.31-20-generic x86_64

Do you have any idea what might be going wrong?

Thanks! Mike

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.

There should be a -s before the subjectID. So the command line is

recon-all -make all -s <subjectID>

Thanks, Sita.

On Wed, 24 Mar 2010, Sita Kakunoori wrote:

Hi Mike,

It seems that it usually happens when the surfaces have been rebuilt and the aparc is out of date (and needs to be rebuilt). Can you try

recon-all -make all <subjectID>

and see if it rebuilds aparc. If you are still having trouble, please feel free to upload the dataset (details in the wiki).

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Thanks, Sita.

On Tue, 23 Mar 2010, Michael Waskom wrote:

...

Hi Sita, all,

I got the rest of the recon to run, made pial edits on the brainmask after autorecon2, and then reran it to the end. It looks like the reconstruction of the cortical surfaces and the inflation worked fine, but the cortical parcellation is totally scrambled. I'm attatching an image of the inflated left hemisphere with the aparc annotation overlay. (It looks much the same on the right hemisphere). I'm also attaching the recon-all.log file. Do you have any idea what might be causing this problem?

Thanks, Mike

On Thu, Mar 18, 2010 at 2:54 PM, Sita Kakunoori sita@nmr.mgh.harvard.eduwrote:

...

Hi Mike,

I don't think the motion artifact could've been causing this error. It's probably a good idea to fix the talairach if you think it's off because if you are reporting the talairach coordinates, you would want the talairach transform to be reasonably accurate.

Sita.

On Thu, 18 Mar 2010, Michael Waskom wrote:

Hi Sita,

...

Running it with the -no-wsgcaatlas seems to do the trick as far as avoiding a segmentation fault. The T1 looks like it has a some motion artifact--might that be causing problems? I checked the Talairach transform and it looks generally alright, although I think it could be improved with some tweaking. It passed the automatic failure detection each time I ran recon-all, though. Would you recommend trying to improve the transform so that things down the line run more smoothly?

Best, Mike

On Thu, Mar 18, 2010 at 1:22 PM, Sita Kakunoori <sita@nmr.mgh.harvard.edu

...

wrote:

...

Hi Mike,

Did you check the talairach. And how do nu.mgz and T1.mgz look. Also you could probably try running the following command to see if the skull strip step finishes without errors.

recon-all -skullstrip -no-wsgcaatlas -s <subjid>

Sita.

On Thu, 18 Mar 2010, Michael Waskom wrote:

Hi Bruce, Nick,

...

I'm getting a segmentation fault that's crashing recon-all at the start of the watershed during skull-stripping. I've tried this three times, once starting the unpacking stream fresh from the raw dicoms, and it keeps happening at exactly the same place. I've been reconstructing brains of other subjects in the same directory all the while, so I don't think it's a permissions issue of any sort.

Full recon-all log is atatched, but here's the section where it crashes:

*************************WATERSHED************************** Sorting... first estimation of the COG coord: x=116 y=166 z=95 r=51 first estimation of the main basin volume: 585576 voxelsSegmentation fault Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010

And here's the OS data from the bugr script:

FREESURFER_HOME: /software/Freesurfer/4.4.0

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0

Debian version: squeeze/sid

Kernel info: Linux 2.6.31-20-generic x86_64

Do you have any idea what might be going wrong?

Thanks! Mike

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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