Hi Michelle - Your column-formatted gradient table (original_columns.bvec) shows up as having only 2 rows in unix (e.g. with the cat command). That's sometimes the case for text files saved from Excel or other non-unix applications. When I open your file in TextEdit on a mac and then copy-paste it into a unix text editor, it shows up fine.
For row-formatted gradient tables, you have to make sure you have the latest version of tracula, as that option was added more recently: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
Hope this helps, a.y
On Thu, 28 Aug 2014, Michele Cavallari wrote:
Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments:
- original bvecs and bvals files organized in rows and columns
- bvecs and bvals files generated by tracula
- error logs
Let me know if you need any other information. Thanks in advance for your help.