The error message is data and bvals/bvecs do not contain the same number
of entries. This doesn't necessarily mean that the bvecs and bvals don't
agree with each other, but that the bvecs and bvals don't agree with the
DWI data.
Based on this line in the log file, there are 130 frames in
ERROR: Found 130 b-values but 108.333 gradient vectors
If the b-value table has 130 entries, then the gradient table should have
130*3 entries (one x,y,z direction vector for each b-value). This error
means that there are fewer entries in the gradient table than there should
be. Run wc -w on
Thank you once again!
Yes, that is true.
The bval and bvec file were doubled, so I removed half the values (and also the
empty spaces) and the fMRIframe: frame = nframes stopped from happening.
A converted the dcm to nii using dcm2nii software, and used its bval and bvec
files as input to
Hi,
Thanks a lot.
I corrected the files as you suggested and now it finished without error.
Best,
Pedro Rosa.
On Jul 4, 2014, at 7:24 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
ERROR: Found 130 b-values but 108.333 gradient vectors
If the b-value table has 130 entries, then the
Hi Pedro - Have you specified not to do eddy current compensation? It
looks like it's being skipped. In that case, you need to also skip the QA
step (by adding -noqa to your trac-all command line). That's because the
QA step requires the output of the eddy current compensation to assess how
There are probably some empty spaces at the end of the lines of the
original files that confuses it into introducing those zeros. If you
attach the original files, I can take a look at them.
On Wed, 2 Jul 2014, Jun Shinozaki wrote:
Hi Anastasia,
I created bvals.txt and bvecs.txt using
Anastasia,
I was finding the same error as Jun, and your help fixed it. Thank you very
much.
However, I am now finding a new error (attached).
Can you help me?
Thank you again.
Regards,
Pedro Rosa.
On Wednesday, July 2, 2014 at 10:49 PM, Jun Shinozaki wrote:
Hi Anastasia,
You are right!
Hi Jun - By a simple word count on these files:
% wc -w bvals bvecs
65 bvals
198 bvecs
263 total
As you can see, there are 3 extra entries in the bvecs file. If you then
open the file, you'll see that there is an extra column of zeros in the
end. Not sure if that's what's causing the
Hi Anastasia,
I created bvals.txt and bvecs.txt using dcm2nii.
These original files were text files and set in dmrirc profile as
set bvalfile = /path/to/bvals.txt.
I checked word count for these files
# wc -w bvals.txt bvecs.txt
65 bvals.txt
195 bvecs.txt
260 total
However, when I run
Hi Jun - It's failing at the point where it tries to extract the low-b
images from the DWI series. I suspect that the number of frames in the 4D
DWI volume that is extracted from your dicom does not match the number of
frames that it expects to find based on how many gradient vectors or
Hi Anastasia,
Thank you for your e-mail.
I took 65 DWIs (5 b0 volumes and 60 direction DWIs).
I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had 65 images.
Also, I checked bvals and bvecs in the dmri folder, and they have 65 counts.
It seems consistent.
I attach bvals and bvecs. These
Dear All,
I am trying to run a single subject in TRACULA (trac-all -prep -c
dmrirc), but exited with ERRORS.
ERROR: fMRIframe: frame = nframes
The attached file is a log file.
Can anyone help me?
Thank you in advance.
Regards,
Jun Shinozaki.
[root@localhost 140518MS]# trac-all -prep -c dmrirc
12 matches
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