philips 3T achieva last gen. not the new one with optical coils. why do you ask? j
On Thu, 22 May 2014, Matt Glasser wrote:
> What kind of scanner do you have?
>
> Peace,
>
> Matt.
>
> From: Jeff Stevenson <[log in to unmask]>
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
> Date: Thursday, May 22, 2014 at 7:56 AM
> To: <[log in to unmask]>
> Subject: Re: [FSL] multi-shell
>
> 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
>
>
>
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