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
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
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.eduwrote:
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.
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 PfuhlThe 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.
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.eduwrote:
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 isrun 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 ordwri-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 PfuhlThe 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.
If you upload these files for me, I can check what's going on: yourDWIs.nii.gz your.ecclog your.bvals
You can upload them for me here: https://gate.nmr.mgh.harvard.edu/filedrop2/
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.
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.
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.eduwrote:
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, because5.2 doesn't run dmri_motion at all.
When you run dmri_motion on the command line, do you use the samesyntax 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 (seeattachment) 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 whendmri_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 runtrac-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. runsfine, 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 theperson 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.
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.
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.eduwrote:
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, itruns 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 wasproduced:
AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 1.74706 0.0119408 0 1 I tried this both on a mac and a linux machine and got the sameresult. 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 --bvalyour.bvals --out output.txt
as well as trac-all -qa -c dmrirc_file with location of bvalspecified 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 in5.2, because 5.2 doesn't run dmri_motion at all.
When you run dmri_motion on the command line, do youuse 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 5.3occur 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 stillcannot 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 in5.2. 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 onlyfor 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.
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Gerit Pfuhl