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

much motion there is in the data.

Hope this helps,

a.y

On Thu, 3 Jul 2014, Pedro Rosa wrote:

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! There are empty spaces at the end of the lines in
original bvecs and bvals.
I could fix the error and finish trac-preproc without error by
eliminating these spaces.
Thank you so much!

Regards,
Jun Shinozaki

2014-07-02 15:21 GMT+09:00 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>:

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 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 "trac-all -prep -c dmrirc", then freesurfer creates
bvals and bvecs automatically in dmri folder.

Then, I check word count
# wc -w bvals bvecs
65 bvals
198 bvecs
263 total

Now, freesurfer adds 3 extra entries in the bvecs file.
As you said, there is an extra column of zeros in the end.

So, I cannot fix the error.

Regards,
Jun Shinozaki

2014-07-01 15:56 GMT+09:00 Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu>:

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 problem, but you might
want to
look for empty lines at the end of your original gradient table.

a.y

On Tue, 1 Jul 2014, Jun Shinozaki wrote:

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 files were created by
freesurfer automatically.

Regards,
Jun Shinozaki

2014-06-30 18:38 GMT+09:00 Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu>:

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
b-values it's looking for. So I'd check these DWI,
gradient vector and
b-value files to make sure they are all consistent.

Hope this helps,
a.y

On Mon, 30 Jun 2014, Jun Shinozaki wrote:

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.

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