Hi Gerit - When I run dmri_motion on the files that you sent me, it runs fine. This is the command line I ran:

dmri_motion --dwi dwi_orig.nii.gz --mat dwi.ecclog --bval bvals --out dwi_motion.txt

And these are the contents of the dwi_motion.txt file that was produced:

AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore
1.74706 0.0119408 0 1

I tried this both on a mac and a linux machine and got the same result. Sorry but I cannot replicate your error.

a.y

On Thu, 20 Feb 2014, Gerit Pfuhl wrote:

tried adopted version of

dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals --out output.txt

as well as trac-all -qa -c dmrirc_file with location of bval specified and trac-all -prep -c, respectively


On 20 February 2014 21:16, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

      Then it's no surprise that the error doesn't occur in 5.2, because 5.2 doesn't run dmri_motion at
      all.

      When you run dmri_motion on the command line, do you use the same syntax as the one you're showing
      below?

      On Thu, 20 Feb 2014, Gerit Pfuhl wrote:

            yes,
            it happens at trac-all -qa after loading the *.nii file (see attachment) or when run as 
            dmri_motion --dwi dwi_orig.nii.gz --mat dwi.ecclog --bval dmri/bvals --out dwi_motion.txt
            immediately.




            On 20 February 2014 17:08, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

                  Does the error in trac-all -prep with 5.3 occur when dmri_motion is run or at a
            different step?

                  On Thu, 20 Feb 2014, Gerit Pfuhl wrote:

                        Dear Tracula Experts,
                        after careful checking we still cannot run trac-all -qa or dwri-motion as the
            command
                        always returns: could not
                        open bvals but the same file is flawlessy opened/retrieved in version 5.2.

                        [cat bvals is fine, trac-all -prep in 5.2. runs fine, trac-all -prep in 5.3
            returns could
                        not open bvals]

                        Kind regards
                        Gerit Pfuhl







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