Hi Sal - Right now you'd just have to try it on one data set and look at the eigenvectors of the tensor (display dmri/dtifit_V1.nii.gz as lines) to make sure they're pointing in the right way.
I'm hoping for the next freesurfer release to finally get mri_convert to read gradient vectors off the dicom header in a way that ends this gradient flipping madness once and for all. But for now you just have to check before you proceed, sorry!
a.y On Wed, 7 Aug 2013, Salil Soman wrote:
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 . 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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