Hi Peter - The format for the bvec and bval files is explained in:
$FREESURFER_HOME/bin/dmrirc.example
If you've structured your dmrirc following this example file and you're
still getting this error, please send the following so I can debug this:
- your exact trac-all command line
- your dmrirc file
- your trac-all.log
- the actual bvecs and bvals files that you specify in your dmrirc
Thanks,
a.y
On Mon, 28 Nov 2011, Peter J. Molfese wrote:
> Sorry for the delay in responding, I wanted to try every permutation that I
> could think of. I updated the tracula binaries for snow leopard
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.html)
> and that gives me some of the same, and some different issues that may help.
> First, if the bvec file is in the correct format (3 columns), then it copies
> the file correctly and trac-all continues smoothly. If the file is in the 3
> row format (needing to be transposed), then tracula will only copy the first
> 9 numbers out of it giving the error of not having the correct number of
> bvecs to bvals. So that seems fixable, I just need to reorient all of our
> bval and bvec files into the correct format.
>
> I'm still a bit unsure why tracula won't create the bvec and bval files
> during the mri_convert stage. I have been using dcm2nii to create these two
> files but then continue to give tracula the path to the dicom files. So the
> orientation of this file could be related to how dcm2nii writes the files.
> Any suggestions would be very welcome. As it stands, my current workflow is:
>
> 1. use dcm2nii to create bvec and bval files
> 2. reorient bvec and bval files to be 3 column and 1 column format
> respectively.
> 3. run trac-all -prep with a config file showing where the dicom images are
> and hand specifying the bvec and bval files
>
> Peter
>
>
> Peter J. Molfese, Ph.D.
> Postdoctoral Associate
> Haskins Laboratories
> 300 George Street, Suite 900
> New Haven, CT 06511
> peter.molf...@yale.edu
>
>
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