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Thanks a lot Matteo. That seems to be the problem. Regards, Nabin On Mon, May 11, 2015 at 1:09 PM, Matteo Bastiani < [log in to unmask]> wrote: > 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 >