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 <
ayend...@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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-- 
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
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