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
- 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.