Hi Anastasia - I attacked the screenshots.

Thanks,


Stefano



----Messaggio originale----
Da: ayendiki@nmr.mgh.harvard.edu
Data: 22-mar-2013 1.39
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts


Hi Stefano - There's nothing in these screenshots that tells you that the
eigenvectors are correct. These are vectors, so the way to check them is
to display them as lines. You display dtifit_V1 as lines, overlaid on
dtifit_FA. Then you see if the lines point in the right direction.

a.y

On Fri, 22 Mar 2013, stdp82@virgilio.it wrote:

> Here they are attacked.
> Thanks,
>
>
> Stefano
>
>
>
>
> ----Messaggio originale----
> Da: ayendiki@nmr.mgh.harvard.edu
> Data: 21-mar-2013 21.50
> A: <stdp82@virgilio.it>
> Cc: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or
> lacking tracts
>
>
> Can you send a screenshot that shows dtifit_V1 and dtifit_FA?
>
> On Thu, 21 Mar 2013, stdp82@virgilio.it wrote:
>
> > I have checked the gradient directions. How can I resolve the brain mask
> > problem. 
> > Can I send you my files of this subject?
> > Stefano
> >
> >
> >
> > ----Messaggio originale----
> > Da: ayendiki@nmr.mgh.harvard.edu
> > Data: 20-mar-2013 22.46
> > A: <stdp82@virgilio.it>
> > Cc: <freesurfer@nmr.mgh.harvard.edu>
> > Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or
> lacking
> > tracts
> >
> >
> > There are chunks of the brain missing from the brain mask. This may cause
> > some tracts to be incomplete or missing.
> >
> > But you should still check that the gradient directions are correct, so
> > you know if you have multiple problems or just one. The FA map can't tell
> > you if the gradient table was correct, you have to check the eigenvectors
> > in dtifit_V1 for that.
> >
> >
> > On Wed, 20 Mar 2013, stdp82@virgilio.it wrote:
> >
> > > File attacked
> > >
> > > ----Messaggio originale----
> > > Da: stdp82@virgilio.it
> > > Data: 20-mar-2013 22.34
> > > A: <ayendiki@nmr.mgh.harvard.edu>
> > > Cc: <freesurfer@nmr.mgh.harvard.edu>
> > > Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking
> > tracts
> > >
> > > 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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> > > > > 
> > > > > 
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