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Dear Mark,
 
Thanks for your replies. The steps in my preprocessing analisis are:
 
1.- I have a 4D nifty image with 16 volumes (first volume is a simple 3D image (T2) without diffusion-weighted (i.e. b=0 s/mm2); the others 15 volumes are b=800 s/mm2 (i.e. gradient volumes).

2.- I need a nodif_brain_mask.nii for dtifit process so ,the first step is to extract the first volume (i.e. the T2, b=0 s/mm2) as the referent volume. This process (extract the first volume = nodif) is Fslroi:

fslroi <sto1.nii.gz> nodif 0 1

3.- In order to create a mask in this nodif i run BET and i get nodif_brain.nii.

bet nodif nodif_brain -m

4.- BET creates a mask (nodif_brain) but it's not exactly the same dimensions as the nodif. So, BET2 modifies the nodif_brain and creates the nodif_brain_mask:

bet2 <sto1.nii.gz> nodif_brain_mask -f 0.3

5.- Then i run eddy current correction:

eddy_correct <sto1.nii.gz> data 0

Is this preprocessing correct in order to run dtifit with this data?

Thanks again,

Patricia.

2011/1/17 Mark Jenkinson <[log in to unmask]>
Dear Patricia,

I'm still not sure what "adjusting the mask to the original image"
does.  Can you be more specific about which images you run
BET and BET2 on and how these are used later on?

All the best,
       Mark


On 17 Jan 2011, at 15:59, Patricia Pires wrote:

> Dear Mark,
>
> I use bet2 to adjuts the mask to the original image.
>
> I am seeing in the website that eddy current is first than bet but I have already run all the study by eddy at the end of the preprocessing. Can this affect my results? Should I run it again or it is not necessary?
>
> Thanks,
>
> Patricia.
>
>
> 2011/1/17 Mark Jenkinson <[log in to unmask]>
> Dear Patricia,
>
> The recommended order on the website I sent was eddy_correct and then bet.
> If you running fslroi too then have this first (so fslroi, then eddy_correct and then bet).
>
> Also, why are you running bet2?
>
> All the best,
>        Mark
>
>
> On 17 Jan 2011, at 14:22, Patricia Pires wrote:
>
> > Hi Mark,
> >
> > i am doing these steps in preprocessing for dtifit analisys or tractography. I proceed fslroi, bet and bet2 just for construct the nodif_brain_mask in my 4D image; then i apply eddy current correction in the original 4D image to get the data for dtifit/tractography.
> >
> > Is that correct?
> >
> > Thank you,
> >
> > Patricia.
> >
> > 2011/1/17 Mark Jenkinson <[log in to unmask]>
> > Hi,
> >
> > Are you trying to do an analysis of diffusion data?
> > If so see:
> >  http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_pipeline.html
> >
> > I'm not sure what reason you are doing the fslroi extraction
> > for, but if it is to remove excessive neck from the image then
> > I would do that first, before anything else, as you have it here.
> >
> > Also, why are you using bet2?
> >
> > All the best,
> >        Mark
> >
> >
> > On 17 Jan 2011, at 08:57, SUBSCRIBE FSL Patricia Pires wrote:
> >
> > > Hello fslexperts,
> > >
> > > i wondering if preprocessing is correct if i follow these steps:
> > >
> > > 1) Fslroi extraction
> > > 2) Bet
> > > 3) Bet 2
> > > 4) Eddy current correction
> > >
> > > I have proceeded in this order for my studies, is that correct or eddy current correction must to be the firt step.
> > >
> > > Thank you very much.
> > >
> > > Patricia.
> > >
> >
>