[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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in Trac-All Pre-Processing step
External Email - Use Caution 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 < ayend...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jocelyn Ra < > jocelyn...@yale.edu> > *Sent:* Monday, June 29, 2020 11:08 AM > *To:* 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.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in Trac-All Pre-Processing step
External Email - Use Caution Hi Anastasia, I'm using FSL 6! Hope this helps, Jocelyn On Thu, Jul 23, 2020 at 8:47 AM Yendiki, Anastasia 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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jocelyn Ra < > jocelyn...@yale.edu> > *Sent:* Wednesday, July 8, 2020 7:22 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Error in Trac-All Pre-Processing step > > > External Email - Use Caution > > 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 < > ayend...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jocelyn Ra < > jocelyn...@yale.edu> > *Sent:* Monday, June 29, 2020 11:08 AM > *To:* 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.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
