Hi there - I think I know what it is, but it's a problem that should be solved if you have the last tracula update. It means that your LANG environment variable needs to be set to en_US.UTF-8, which the update does for you.

a.y

On Tue, 5 Jul 2016, Lars M. Rimol wrote:

Hi Anastasia,

I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the generated bvec file has commas instead of full stop (0,832 instead of 0.832). The input file (attached: "bvec_rows") has full stop. Another thing is that the generated bvals file has an empty space at the end of the row, which is not there in the input file ("bvals_rows").

thank you!

LMR

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and dmri/bvecs files that get generated look fine too?

a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:

Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating that there are different numbers of entries in the bval and bvec files. I do n't understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9).

Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.n ii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 U TC 2015 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

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I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

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The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot =  /media/lmr2/subjects/DTI set dcmlist =   ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv

Thank you!

yours,

Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

sincerely yours,

Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway