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.

1) 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

trac-all.log

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