Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Anastasia Yendiki]

Hi there - I think I know what it is, but it's a problem that should be 
solved if you have the last tracula update. It means that your LANG 
environment variable needs to be set to en_US.UTF-8, which the update does 
for you.


a.y

On Tue, 5 Jul 2016, Lars M. Rimol wrote:



Hi Anastasia,

I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
is that the generated bvals file has an empty space at the end of the row,
which is not there in the input file ("bvals_rows").



thank you!

LMR

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals
and dmri/bvecs files that get generated look fine too?

a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:

Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
that there are different numbers of entries in the bval and bvec files. I do

n't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
Tracula and FSL (v 5.0.9).



Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.n

ii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o

/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 U
TC 
2015 x86_64 x86_64 x86_64 GNU/Linux


trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this 
error message is indicative of some other problem. Is the updated Tracula

version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway










sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Lars M. Rimol]

Hi Anastasia,

I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
is that the generated bvals file has an empty space at the end of the row,
which is not there in the input file ("bvals_rows").



thank you!

LMR

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and
dmri/bvecs files that get generated look fine too?

a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:


Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating
that there are different numbers of entries in the bval and bvec files. I don't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated
Tracula and FSL (v 5.0.9).


Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC
2015 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this
error message is indicative of some other problem. Is the updated Tracula
version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway











sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway


bvals_rows
Description: Binary data


bvec_rows
Description: Binary data


bvals
Description: Binary data


bvecs
Description: Binary data


dwi_orig.mghdti.bvals
Description: Binary data


dwi_orig.mghdti.bvecs
Description: Binary data
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Anastasia Yendiki]

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals 
and dmri/bvecs files that get generated look fine too?


a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:


Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
that there are different numbers of entries in the bval and bvec files. I don't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
Tracula and FSL (v 5.0.9).


Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 
2015 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this 
error message is indicative of some other problem. Is the updated Tracula
version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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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
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Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Koubiyr, Ismail]

Hi Lars,

I had the same problem. You can notice in your bvec file that there are some 
unusual blank spaces sometimes. Try to look at each space between two numbers 
and make sure it’s fine. You can also make sure about the number of entries by 
running wc -w on each of your bvec or bval file.
Hope it’s gonna help you.

Cheers,

Ismail

> On Jul 2, 2016, at 4:27 AM, Lars M. Rimol  wrote:
> 
> Hi,
> 
> Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
> that there are different numbers of entries in the bval and bvec files. I 
> don't understand why, since both have the same number of rows (64). 
> 
> OS = Ubuntu 14.04.4
> Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
> Tracula and FSL (v 5.0.9). 
> 
> 
> Error message:
> 
> #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
> dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
>  -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o 
> /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
> Error: bvecs and bvals don't have the same number of entries
> Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 
> UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> 
> trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016
> 
> --
> I also tried flipping the bvec/bval files, but got the same error. 
> I don't know if there's anything wrong with the bval/bvec files, or if this 
> error message is indicative of some other problem. Is the updated Tracula 
> version only compatible with the dev version of FS? 
> 
> I have attached the bval/bvec files and the trac-all.log.
> 
> ---
> The contents of the dmric file is:
> 
> setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
> set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
> set subjlist = (4_FS)
> set dcmroot =  /media/lmr2/subjects/DTI
> set dcmlist =   ( 4/5/1.dcm )
> set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
> set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv
> 
> 
> 
> Thank you!
> 
> 
> yours,
> 
> Lars M. Rimol, PhD
> Senior researcher, 
> Norwegian Advisory Unit for functional MRI
> Department of Radiology, 
> St. Olav's University hospital,
> 7006 Trondheim, 
> Norway
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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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
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Lars M. Rimol]

Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating
that there are different numbers of entries in the bval and bvec files. I
don't understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated
Tracula and FSL (v 5.0.9).


Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
-r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08
UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this
error message is indicative of some other problem. Is the updated Tracula
version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
0100010001000100010001000100010001000100010001000100010001000100010001000100010001000100010001000100010001000100010001000200020002000200020002000200020002000200020002000200020002000200020002000200020002000200020002000200020002000200020002000000
0-0.203770.197880.40243-0.40388-0.20233-0.85342-0.73137-0.40767-0.73256-0.65079-0.32244-0.32447-0.65033-0.97858-0.854560.000732920.00315550.654590.329460.198010.204310.651670.324360.200460.403880.732220.728930.852650.857480.97941-0.203830.198380.40215-0.40386-0.20227-0.85391-0.73143-0.40738-0.73222-0.65118-0.32277-0.32447-0.65021-0.97877-0.854070.00107460.00268950.654090.329750.198530.203820.651980.32440.200420.403860.731880.72890.853130.857030.97941000
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bvals
Description: Binary data


bvec
Description: Binary data
lø. 02. juli 09:47:59 +0200 2016
/media/lmr2/subjects/DTI
/usr/local/freesurfer/bin/trac-all
-c dmric_test_mars2015 -prep
Subject 4_FS
SUBJECTS_DIR /media/lmr2/subjects/DTI
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
lmr
dmed4870
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC