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 >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- 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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