Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz  and not in dwi.nii.gz (I have attacked the relative images).


Stefano

----Messaggio originale----
Da: ayendiki@nmr.mgh.harvard.edu
Data: 20-mar-2013 16.40
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts


Hi Stefano - Have you checked that your gradient table is correct by
looking at the output of the tensor fit?

a.y

On Wed, 20 Mar 2013, stdp82@virgilio.it wrote:

> Hi list and Anastasia,
> if you remember the last week I had same problems with tracula output: the  final tract are lacking or
> incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident
> error (you can see this in picture that I have attacked). 
>
> To resolve this issue I have:
>
> 1-checked the correct overlap of dwi and dwi_mask
> 2-rerun data with new version 5.2
> 3-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture
> attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1)
>
> Please, give me an advise
>
> Thanks
>
>
> Stefano
>
>
>
>
> ----Messaggio originale----
> Da: stdp82@virgilio.it
> Data: 12-mar-2013 17.47
> A: <ayendiki@nmr.mgh.harvard.edu>
> Cc: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap
>
> I got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image
> from dlabel/diff/aparc+aseg.bbr.nii
>
>
> Stefano
>
>
>
> ----Messaggio originale----
> Da: ayendiki@nmr.mgh.harvard.edu
> Data: 12-mar-2013 17.19
> A: <stdp82@virgilio.it>
> Cc: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] R: Re:  Question on tracula and dwi-T1 overlap
>
>
> Can you please answer my question? I can't really tell if the issue is due 
> poor dwi-aseg overlap unless you tell me where you got that aseg volume 
> from.
>
> On Tue, 12 Mar 2013, stdp82@virgilio.it wrote:
>
> > Thank you Anastasia. What do you think about the issue in the file attacked
> > (I'm noting that same subjects are lacking of same
> >  tracts or same tracts are incomplete)
> > 
> > 
> > Stefano
> > 
> > 
> > ----Messaggio originale----
> > Da: ayendiki@nmr.mgh.harvard.edu
> > Data: 12-mar-2013 17.02
> > A: <stdp82@virgilio.it>
> > Cc: <freesurfer@nmr.mgh.harvard.edu>
> > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap
> > 
> > 
> > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in
> > the dlabel/diff/ directory has been mapped to the same space as the DWI,
> > so those are the volumes that can be compared directly to dwi.nii.gz.
> > 
> > a.y
> > 
> > On Tue, 12 Mar 2013, stdp82@virgilio.it wrote:
> > 
> > > Hi list,
> > >
> > > I have two questions, please.
> > >
> > > I'm using version 5.1 to complete my analysis.
> > >
> > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same
> > > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg.
> > > How can I resolve this issue? 
> > >
> > > 2-After TRACULA analysis, I'm noting that same subjects are lacking of
> > same
> > > tracts or same tracts are incomplete (figure 3).
> > >
> > > Could it depends from the issue in question 1? I'm thinking to rerun all
> > > using version 5.2 but before starting new analyses, I'd like to ask you
> > > which is the possible error.
> > >
> > >
> > > Stefano
> > >
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