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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edumailto:cnweis@uwm.edu> Sent: Tuesday, January 9, 2018 11:42:07 AM To: freesurfer@nmr.mgh.harvard.edumailto: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

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edumailto:cnweis@uwm.edu> Sent: Tuesday, January 9, 2018 11:42:07 AM To: freesurfer@nmr.mgh.harvard.edumailto: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

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, January 12, 2018 at 2:15 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edumailto: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.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edumailto:cnweis@uwm.edu> Sent: Tuesday, January 9, 2018 11:42:07 AM To: freesurfer@nmr.mgh.harvard.edumailto: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

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

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: Saturday, January 13, 2018 at 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Carissa Nicole Weis <cnweis@uwm.edumailto:cnweis@uwm.edu> Sent: Tuesday, January 9, 2018 11:42:07 AM To: freesurfer@nmr.mgh.harvard.edumailto: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