Hi Carissa – You mentioned that your DWIs had 2mm isotropic resolution, but the data that I received is 1x1x2mm, so it has a larger matrix size. Is there any chance that some form of preprocessing was done that resulted in upsampled data, or was it acquired this way?

Best,
a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 18, 2018 at 2:55 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

I’ve uploaded the data. Just want to confirm you received it.


Thanks,

 

Carissa

 

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Saturday, January 13, 2018 3:49 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

 

Those are pretty standard dimensions, so memory is not likely to be a problem. Can you upload a zip file with this subject's entire TRACULA subject dir for me here: https://gate.nmr.mgh.harvard.edu/filedrop2/

From:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edu>
Sent: Saturday, January 13, 2018 10:14:26 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

 

How much memory would you recommend using? I’ve been using 8gb from our cluster for each step in TRACULA.

 

The diffusion images were acquired with fairly common parameters: 3 B=0 images, 35 different gradient directions at B=800 with 70 slices per direction at a voxel size of 2x2x2mm for a 128x128 matrix.

 

Thanks for your help!

 

Carissa

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, January 12, 2018 at 2:15 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

 

Hi Carissa - One possibility is that you may be running out of memory. What are the dimensions of your diffusion images?

 

a.y

From:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edu>
Sent: Thursday, January 11, 2018 4:55:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

 

Hello Anastasia!

 

I’ve since tried to rerun –bedp with this same subject and the output still did not indicate it had completed.

 

Thanks for your help!

 

Carissa

 

From:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Thursday, January 11, 2018 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

 

Hi Carissa - It loks like bedpost ran fine. Can you please attach your entire log file (scripts/trac-all.log)? It's hard to tell what went wrong just from the end of it.

 

Best,

a.y

From:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edu>
Sent: Tuesday, January 9, 2018 11:42:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

 

Hello all,

 

I’ve been running trac-all from the command line without the configuration file since I’m not changing any defaults. I’ve successfully run several subjects through the trac-all –prep stage, and the –bedp stage. **Although I never got the “trac-all –bedp finished without error” prompt in the -bedp terminal output and usually just get something that says at the end:

 

../freesurfer_6.0/bin/bedpost_mgh: line 440: 46773 Terminated   ${subjdir}.bedpostX/monitor

 

OR it’ll make it to something like…

 

37 slices processed

38 slices processed

Queuing post processing stage

46 slices processed

 

…and that’s as far as the output in the terminal goes.

 

It appears all the expected files have been created in dmri.bedpostx/ so I was assuming this step had been completed. However, when I go to run the –paths step I get an error that says:

 

Loading DWIs from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/dmri/dwi.nii.gz

Loading mask from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dlabel/diff/aparc+aseg_mask.bbr.nii.gz

Loading BEDPOST parameter samples from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri.bedpostX

Loading b-values from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvals

Loading gradients from /bigraid-03/LS/OtherStudies/larson_buffalo/MRI7/KAward/CWEIS_DTI/sub243/sub243/dmri/bvecs

INFO: Found 3 baseline images (b = 0) out of a total of 38 frames

Segmentation fault

Linux compute-026.mortimer 2.6.32-696.18.7.e16.x86_64 #1 SMP Thu Jan 4 17:31:22 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

 

trac-paths exited with ERRORS at Tue Jan 9 09:34:58 CST 2018

 

 

I’ve checked the mask and it looks fine. I can’t imagine the bvals and bvecs files should be the issue since I already made it through the –prep stage. Is it something with my bedpost outputs??

 

Thanks for your help!

 

Carissa