Thank you for the email.

I saw a warning to check for flipping L-R from the dcm2nii site:

http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html

Is the problem you mentioned vendor specific (I have all GE data). Is there a different tool you would recommend for generating the bvec files? I would prefer to run tracula right off the original dicom images but transferring them to the cluster and anonymizing them would be prohibitively difficult.

I could not find the freesurfer archive message you referred to. Any pointers would be greatly appreciated.

Best wishes,

Sal

On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

set x = `cat bvecs | awk '{if (NR==1) print}'`
set y = `cat bvecs | awk '{if (NR==2) print}'`
set z = `cat bvecs | awk '{if (NR==3) print}'`

@ k = 1
while ( $k <= `head -1 bvecs|wc -w` )
echo $x[$k] $y[$k] $z[$k]
@ k = $k + 1
end

I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I think there was a thread recently that suggested it might.

On Wed, 7 Aug 2013, Salil Soman wrote:

Hi,
I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a
y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under
the impression tracula requires this to be converted to a n row by 3 column file. 1) is this correct, 2) is there a
preferred way to perform this transformation on linux systems?

Thanks you,

-Sal

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