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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