Dear Anastasia,
Thank you for all your assistance.
The problem was the conversion of the gradient table to /dmri/bvecs.norot and /dmri/bvecs. The original table was using the period as the decimal point. However, the environment variable LC_NUMERIC was equal to "pt_BR.UTF-8" (that define how the system format the numbers, for example, the decimal separator, (in Brazil we use a comma (,))) the TRACULA was not able to convert it correctly.
I used the following command to solve this.
$ echo 'export LC_NUMERIC="en_US.UTF-8"' >>~/.bashrc $ source ~/.bashrc
Best wishes, Walter
2017-08-01 17:32 GMT-03:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:
Hi Walter – I’d check on the structural segmentation and its registration to the DWIs. Open dmri/dtifit_FA.nii.gz and label/diff/aparc+aseg.bbr.nii.gz and check if they’re well aligned and if the segmentation looks fine.
On a separate note (and I don’t know if it’s related to the error you’re asking about), TRACULA is expecting the numbers in the gradient tables to have decimal points and yours seem to have commas (see the “printf:” warnings near the beginning of the preprocessing step).
Best,
a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Walter Hugo Lopez Pinaya walhugolp@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 31, 2017 at 1:11 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error: trac-all -prep "Segmentation fault (core dumped)"
Hello FreeSurfer Developers,
I am attempting to compute the tracula preprocessing directive (-prep), but for all my subjects I get the following error when it computes the pathway priors from atlas to T1.
... WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels INFO: Length of center streamline is 9 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 1 INFO: Minimum allowable curvature at a dominant point is 0.070643 INFO: Points where local peeks in curvature occur are 121 129 57 (curv = 0.0819549) INFO: Intermediate dominant points are 123 130 49 123 130 51 123 129 54 122 129 56 120 130 58 *Segmentation fault (core dumped) * Linux hardleste 4.8.0-58-generic #63~16.04.1-Ubuntu SMP Mon Jun 26 18:08:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Qui Jul 27 21:23:25 BRT 2017
I have searched the list and no similar errors with reply have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the trac-all.log and trac-all.error in case it's of any use.
- FreeSurfer version: freesurfer-Linux-centos6_x86_
64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 16.04.2 LTS xenial 3) trac-all.log and trac-all.error: see attached
trac-all.error https://drive.google.com/file/d/0Bz-56qlsQ1xDbjEzZ3NkUG1XVlk/view?usp=drive_web trac-all.log https://drive.google.com/file/d/0Bz-56qlsQ1xDMk1FUHI2QlZkMGc/view?usp=drive_web
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