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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