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:
> 1) original bvecs and bvals files organized in rows and columns
> 2) bvecs and bvals files generated by tracula
> 3) error logs
>
> Let me know if you need any other information.
> Thanks in advance for your help.
>
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