Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts - Freesurfer

21 Mar 2013

      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:
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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:
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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
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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
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...
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
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...
attacked, the .mincost file now contains as first value 0.87 (previous
it was 1.1)
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...
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
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...
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
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...
...
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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