ah! i think i remember you mentioning it at the course here in seattle. something about the head not being fully centered so there is asymmetry in the distribution of the field. right. does not apply to us. so which flags are optimal
for non hcp multi shell? j
On Thu, 22 May 2014, Saad Jbabdi wrote:
> The gradient nonlinearities are particularly pronounced on the HCP scanner because of the positioning of the table. Have a look at the online HCP doc where this is explained.
>
> Cheers
> Saad
>
>
> On 22 May 2014, at 15:56, Jeff Stevenson <[log in to unmask]> wrote:
>
> Ah! Is that appropriate only for hcp protocols or useful in my case? J
>
> Sent from my iPhone
>
> On May 22, 2014, at 6:39 AM, Saad Jbabdi <[log in to unmask]> wrote:
>
> No, this file is generated by the HCP pre-processing pipeline. Then it is used by DTIFIT and BEDPOSTX to correct the bvals/bvecs on a voxelwise basis.
> Cheers
> Saad.
>
>
> On 22 May 2014, at 14:25, Jeff Stevenson <[log in to unmask]> wrote:
>
> Got it. And the -cgradnonlin option is the flag that generates it?
> J
>
> Sent from my iPhone
>
> On May 22, 2014, at 6:15 AM, Saad Jbabdi <[log in to unmask]> wrote:
>
> If you mean the theory behind it then it¢s from this paper: http://onlinelibrary.wiley.com/doi/10.1002/mrm.10545/abstract
>
>
> On 22 May 2014, at 14:06, Jeff Stevenson <[log in to unmask]> wrote:
>
> And I am still trying to figure out where the grad_dev comes from:-). J
>
>
> Sent from my iPhone
>
> On May 22, 2014, at 5:08 AM, Nele De Witte <[log in to unmask]> wrote:
>
> Dear Saad (and others)
>
> You said that you also need the gradnonlin option in dtifit, so I tried the following command:
> dtifit --data=data.nii.gz --out=dtifit --mask=nodif_brain_mask.nii.gz --bvecs=bvecs --bvals=bvals
> --gradnonlin=grad_dev.nii.gz
>
> It starts running, but then after a while the terminal says 'Killed' (I tried it twice and I got the same result in both occasions). Why is this? What am I doing wrong?
>
> Thanks!
>
> Nele
>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>
>
>
|