On Friday, July 4, 2014 at 5:18 AM, Anastasia Yendiki wrote:

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 the DWI

dicoms, so I suspect that you may have two repetitions of your 65

directions:

INFO: (120 120 50), nframes = 130, ismosaic=0

You can confirm this my looking at the images. If that is the case, you

need to have two repetitions in the bvecs/bvals files too.

On Thu, 3 Jul 2014, Pedro Rosa wrote:

Hi!

Thanks! It helped, but now I have another error…

I attached the log, and both the bvec and bval files that served as inputs

(without any empty space in the end) and the ones generated by the script in

the $subject/dmri (which turns out to have empty spaces in the end). All

these 4 files have 65 entries (bval with 65 for each one of the three

sequences).

Can you spot the error?

Regards

Pedro Rosa

On Thursday, July 3, 2014 at 3:05 AM, Anastasia Yendiki wrote:

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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