Hi Anastasia,

I attach the bvecs that I'm using. The second is produced in the dmri.
You are noting that the first is in 3 rows, the second contains only 3 row with a 0

This is the last error
fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1
fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz
bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff
#-------------------------------------
#@# Inter-subject registration Gio 31 Gen 2013 22:40:26 CET
flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfo
convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat
#-------------------------------------
#@# Masks Gio 31 Gen 2013 22:41:55 CET
#-------------------------------------
#@# Tensor fit Gio 31 Gen 2013 22:41:55 CET
dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Gio 31 Gen 2013 22:42:02 CET

Thanks,


Stefano



----Messaggio originale----
Da: ayendiki@nmr.mgh.harvard.edu
Data: 31-gen-2013 21.43
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] bvecs tracula


Hi Stefano - Are the original bvecs (that you specify in your
configuration file) arranged in 3 rows or 3 columns?

a.y

On Thu, 31 Jan 2013, stdp82@virgilio.it wrote:

> Hi list,
> I'm running trac-all -prep -c
>
> but I have this error
>
> dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m
> /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r
> /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b
> /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o
> /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit
> Error: bvecs and bvals don't have the same number of entries
>
> I'm noting that my original bvecs are
>
> 0  -0.460  -0.539   0.490  -0.071   0.226   0.463   0.483  -0.643   0.468  -0.730  -0.707  -0.318   0.175   0.488   0.460
> 0  -0.395  -0.588  -0.706  -0.605  -0.607  -0.236  -0.180  -0.464  -0.562  -0.337  -0.699  -0.786  -0.786  -0.712  -0.301
> 0  -0.795   0.419  -0.057  -0.793  -0.725  -0.708  -0.695  -0.609   0.333   0.413  -0.108   0.368   0.392  -0.004   0.476
>
> and in dmri 
>
> 0
> 0
> 0
>
> bvals conversion is ok. What's happen? Why are there an error about conversion to FSL format?
>
> Thank you very much, I really appreciate your patience.
>
> Stefano
>
>
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