I even did chmod 777, but that did not help either, tried various subjects, various locations of the bvals file. Even checked that the folders have rwx permissions
Default is read and write permission. And trac-all -prep in version 5.2.0 reads and writes in the same folder.
I can open and read the file with cat or edit with mcedit.


On 21 February 2014 18:34, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Gerit - The dmri/bvals file is created by trac-all (by transforming the original gradient vectors to account for the eddy current correction). So it's not an input file that you specify anywhere, it's an output of trac-all. Do you have read permmission to that file?

a.y


On Fri, 21 Feb 2014, Gerit Pfuhl wrote:

Hi,
thanks, no doubt that the files are okay, it must be something in how tracula is set up I supose because this is
the report we get:

File exists, open returns return-value 3 -> Error-Message from dmri_motion wrong
atlas1:/fastfs/dolescha/pfuhl # strace dmri_motion --dwi
/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/dwi_orig.nii.gz --mat
/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/dwi.ecclog --bval /fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bvals
--out dwi_motion.txt
...
write(1, "Loading b-value table from /fast"..., 78Loading b-value table from
/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bvals
) = 78
open("/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bvals", O_RDONLY) = 3
write(1, "ERROR: Could not open /fastfs/ig"..., 85ERROR: Could not open
/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bvals for reading

2) File does not exist (missing s), open returns -1 as return-value -> Error-Message from dmri_motion correct.
 strace dmri_motion --dwi /fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/dwi_orig.nii.gz --mat
/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/dwi.ecclog --bval /fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bval
--out dwi_motion.txt
...
write(1, "Loading b-value table from /fast"..., 77Loading b-value table from
/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bval
) = 77
open("/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bval", O_RDONLY) = -1 ENOENT (No such file or directory)
write(1, "ERROR: Could not open /fastfs/ig"..., 84ERROR: Could not open
/fastfs/igis/MRI_fs_rec_dti/64-23-145-1/dmri/bval for reading
) = 84
exit_group(1) 

I just tried it again. Any way to specify bvals elsewhere?

Thanks
Gerit


On 21 February 2014 18:04, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

      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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