Dear Nabin,

are you working in the directory where you have all those files?
Otherwise, try to include the full path to each file before launching dtifit (e.g., --bvecs=/data/subj1/bvecs --bvals=/data/subj1/bvals).


Cheers,
Matteo

> On 11 May 2015, at 09:58, Nabin Koirala <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> I am trying to do DTIfit using the command line but it shows me the error " could not open matrix file bvecs. could not open matrrxi file bvals, Error:bvecs must be either 3XN or NX3" .
>
> I try running it from GUI from which it runs fine, the problem is only with command line.
>
> The command line is as follows:
>
> dtifit --data=$1_eddy.nii.gz --mask=$1_brain_mask.nii.gz --bvecs=bvecs --bvals=bvals --out=dtifit_result
>
> Your suggestions would be really helpful.
>
> Many thanks in advance.
>
> Regards,
> Nabin