Hi Jocelyn - I'm having a hard time replicating this error. What version of FSL are you using? You can see this in the file $FSLDIR/etc/fslversion.

Thanks!

a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jocelyn Ra jocelyn.ra@yale.edu Sent: Wednesday, July 8, 2020 7:22 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in Trac-All Pre-Processing step

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Hi Anastasia!

Thank you for taking the time to help me with this! I will send along the trac-all.log file for my run directly to you via email, since my previous attempts to post it were rejected by the Freesurfer mailing list moderators.

Thank you once again! Sincerely, Jocelyn

On Tue, Jun 30, 2020 at 12:51 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Jocelyn - It's strange to get this in the tutorial data, it's the kind of thing you might get if the FS recon was missing part of the brain or if the alignment between datasets was not good. So I'm surprised you're getting this in the tutorial data. Can you please send your entire trac-all.log file?

Thanks! 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 Jocelyn Ra <jocelyn.ra@yale.edumailto:jocelyn.ra@yale.edu> Sent: Monday, June 29, 2020 11:08 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Error in Trac-All Pre-Processing step

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Hi all,

After running the trac-all command in the pre-processing step in the official TRACULA tutorial, I ran into the following error:

WARN: Could not find satisfactory control point fit - try 4718 Writing output files to /home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_* Writing spline volume to /home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz Segmentation fault

The "WARN" message repeated several times before this final message, making me believe the issue is with the control points. For reference, I am using the tutorial data set, "set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)" for the control points, and LINUX.

Has anyone else run into this error, and could someone please help me with this issue?

Thank you in advance! Sincerely, Jocelyn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Jocelyn - Although we could not replicate your error here, the error message mentions MKL, which is the Intel math kernel library. In case this library was not installed properly on your system, you can try (re)installing it from here:

https://software.intel.com/content/www/us/en/develop/articles/intel-math-ker...

Let us know how it goes!

a.y

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jocelyn Ra jocelyn.ra@yale.edu Sent: Thursday, July 23, 2020 1:26 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in Trac-All Pre-Processing step

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Hi Anastasia,

I'm using FSL 6!

Hope this helps, Jocelyn

On Thu, Jul 23, 2020 at 8:47 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Jocelyn - I'm having a hard time replicating this error. What version of FSL are you using? You can see this in the file $FSLDIR/etc/fslversion.

Thanks!

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 Jocelyn Ra <jocelyn.ra@yale.edumailto:jocelyn.ra@yale.edu> Sent: Wednesday, July 8, 2020 7:22 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in Trac-All Pre-Processing step

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Hi Anastasia!

Thank you for taking the time to help me with this! I will send along the trac-all.log file for my run directly to you via email, since my previous attempts to post it were rejected by the Freesurfer mailing list moderators.

Thank you once again! Sincerely, Jocelyn

On Tue, Jun 30, 2020 at 12:51 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Jocelyn - It's strange to get this in the tutorial data, it's the kind of thing you might get if the FS recon was missing part of the brain or if the alignment between datasets was not good. So I'm surprised you're getting this in the tutorial data. Can you please send your entire trac-all.log file?

Thanks! 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 Jocelyn Ra <jocelyn.ra@yale.edumailto:jocelyn.ra@yale.edu> Sent: Monday, June 29, 2020 11:08 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Error in Trac-All Pre-Processing step

External Email - Use Caution

Hi all,

After running the trac-all command in the pre-processing step in the official TRACULA tutorial, I ran into the following error:

WARN: Could not find satisfactory control point fit - try 4718 Writing output files to /home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_* Writing spline volume to /home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz Segmentation fault

The "WARN" message repeated several times before this final message, making me believe the issue is with the control points. For reference, I am using the tutorial data set, "set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)" for the control points, and LINUX.

Has anyone else run into this error, and could someone please help me with this issue?

Thank you in advance! Sincerely, Jocelyn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer