As a sanity check, you can downsample one of the data sets that fail to 2mm iso, and see if it runs that way. This would tell you if it's a data size issue.

From: Carissa Nicole Weis <cnweis@uwm.edu>
Sent: Monday, January 29, 2018 5:53:59 PM
To: Yendiki, Anastasia
Subject: RE: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?
 

I went back and checked and it was just a mistake in our paperwork. All of the subjects’ data were acquired at 1x1x2 resolution, but for some reason some of the subjects would run through bedp on the first pass while others required several passes. I’ve requested additional memory on our cluster to run the subjects who stalled, but that didn’t make a difference. If you don’t see any potential issues from your end, then I’m beginning to think it could be a technical issue with our cluster perhaps it’s timing out or freezing after running for too long. I’ll look into this more to see if I can find any issues there.

 

Do you have any other recommendations for troubleshooting at this point?

 

Thanks,

 

Carissa

 

From: Yendiki, Anastasia [mailto:AYENDIKI@mgh.harvard.edu]
Sent: Monday, January 29, 2018 1:54 PM
To: Carissa Nicole Weis <cnweis@uwm.edu>
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

 

The subjects that run through with no problems have 2mm isotropic resolution and the subjects that give you the segmentation fault have higher resolution? Then it sounds like a problem of insufficient memory.

From: Carissa Nicole Weis <cnweis@uwm.edu>
Sent: Sunday, January 28, 2018 9:44:08 PM
To: Yendiki, Anastasia
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

 

My mistake. It was acquired that way.

 

Also, after running my subjects through the -bedp step several times I’ve now only got one subject who is lingering there, but some subjects had to run 7+ times through bedp before finishing properly. I do have another dataset to analyze that was acquired with the same parameters so it’s quite possible this issue may arise again.  

 

Thanks again for your help,

 

Carissa

 

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