[Freesurfer] Problem with tracula: incomplete or lacking tracts

2013-03-28 Thread stdp82
 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, std...@virgilio.it wrote:
  
File attacked
   
Messaggio originale
Da: std...@virgilio.it
Data: 20-mar-2013 22.34
A: ayend...@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: ayend...@nmr.mgh.harvard.edu
Data: 20-mar-2013 16.40
A: std...@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, std...@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: std...@virgilio.it
 Data: 12-mar-2013 17.47
 A: ayend...@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: ayend...@nmr.mgh.harvard.edu
 Data: 12-mar-2013 17.19
 A: std...@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, std...@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: ayend...@nmr.mgh.harvard.edu
  Data: 12-mar-2013 17.02
  A: std...@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, std...@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

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

2013-03-28 Thread Anastasia Yendiki
 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, std...@virgilio.it wrote:
  
File attacked
   
Messaggio originale
Da: std...@virgilio.it
Data: 20-mar-2013 22.34
A: ayend...@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: ayend...@nmr.mgh.harvard.edu
Data: 20-mar-2013 16.40
A: std...@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, std...@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: std...@virgilio.it
 Data: 12-mar-2013 17.47
 A: ayend...@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: ayend...@nmr.mgh.harvard.edu
 Data: 12-mar-2013 17.19
 A: std...@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, std...@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: ayend...@nmr.mgh.harvard.edu
  Data: 12-mar-2013 17.02
  A: std...@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, std...@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

[Freesurfer] Problem with tracula: incomplete or lacking tracts

2013-03-25 Thread stdp82
Hi Anastasia,
I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is 
possible that it depends from an error in my configuration file?
I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another  one?
Thanks,

Stefano


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

 Thank you Anastasia.
 I'm checking bvecs/bvals. I obtain it by DTI table creator
 (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html)
 
 bvecs/bvals should be done.
 
 Gradients can be the unique responsable?
 
 
 Stefano
 
 
 
 
 Messaggio originale
 Da: ayend...@nmr.mgh.harvard.edu
 Data: 22-mar-2013 17.07
 A: std...@virgilio.it
 Cc: freesurfer@nmr.mgh.harvard.edu
 Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: 
 incomplete or lacking tracts
 
 
 Your gradient table is wrong. See where I've marked the corpus callosum in
 your screenshot. The eigenvectors are not pointing along the corpus
 callosum, but perpendicular to it. So they're off by 90 degrees, which
 means the same is true about the vectors in your gradient table.
 
 On Fri, 22 Mar 2013, std...@virgilio.it wrote:
 
  Hi Anastasia - I attacked the screenshots.
  Thanks,
 
 
  Stefano
 
 
 
  Messaggio originale
  Da: ayend...@nmr.mgh.harvard.edu
  Data: 22-mar-2013 1.39
  A: std...@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, std...@virgilio.it wrote:
 
   Here they are attacked.
   Thanks,
  
  
   Stefano
  
  
  
  
   Messaggio originale
   Da: ayend...@nmr.mgh.harvard.edu
   Data: 21-mar-2013 21.50
   A: std...@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, std...@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: ayend...@nmr.mgh.harvard.edu
Data: 20-mar-2013 22.46
A: std...@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, std...@virgilio.it wrote:
   
 File attacked

 Messaggio originale
 Da: std...@virgilio.it
 Data: 20-mar-2013 22.34
 A: ayend...@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: ayend...@nmr.mgh.harvard.edu
 Data: 20-mar-2013 16.40
 A: std...@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, std...@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: std...@virgilio.it

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

2013-03-25 Thread Anastasia Yendiki


Hi Stefano - As I recall, we established that your bvecs were wrong. Did 
you fix them?


a.y

On Mon, 25 Mar 2013, std...@virgilio.it wrote:


Hi Anastasia,

I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is 
possible that it depends from
an error in my configuration file?

I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another  one?

Thanks,


Stefano



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

 Thank you Anastasia.
 I'm checking bvecs/bvals. I obtain it by DTI table creator
 (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html)

 bvecs/bvals should be done.

 Gradients can be the unique responsable?


 Stefano




 Messaggio originale
 Da: ayend...@nmr.mgh.harvard.edu
 Data: 22-mar-2013 17.07
 A: std...@virgilio.it
 Cc: freesurfer@nmr.mgh.harvard.edu
 Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: 
incomplete or lacking tracts


 Your gradient table is wrong. See where I've marked the corpus callosum in
 your screenshot. The eigenvectors are not pointing along the corpus
 callosum, but perpendicular to it. So they're off by 90 degrees, which
 means the same is true about the vectors in your gradient table.

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

  Hi Anastasia - I attacked the screenshots.
  Thanks,
 
 
  Stefano
 
 
 
  Messaggio originale
  Da: ayend...@nmr.mgh.harvard.edu
  Data: 22-mar-2013 1.39
  A: std...@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, std...@virgilio.it wrote:
 
   Here they are attacked.
   Thanks,
  
  
   Stefano
  
  
  
  
   Messaggio originale
   Da: ayend...@nmr.mgh.harvard.edu
   Data: 21-mar-2013 21.50
   A: std...@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, std...@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: ayend...@nmr.mgh.harvard.edu
Data: 20-mar-2013 22.46
A: std...@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, std...@virgilio.it wrote:
   
 File attacked

 Messaggio originale
 Da: std...@virgilio.it
 Data: 20-mar-2013 22.34
 A: ayend...@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: ayend...@nmr.mgh.harvard.edu
 Data: 20-mar-2013 16.40
 A: std...@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, std...@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

[Freesurfer] Problem with tracula: incomplete or lacking tracts

2013-03-20 Thread stdp82
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_mask2-rerun data with new version 
5.23-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 originaleDa: stdp82@virgilio.itData: 12-mar-2013 17.47A: 
ayend...@nmr.mgh.harvard.eduCc: freesurfer@nmr.mgh.harvard.eduOgg: 
[Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlapI 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: ayend...@nmr.mgh.harvard.edu
Data: 12-mar-2013 17.19
A: std...@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, std...@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: ayend...@nmr.mgh.harvard.edu
 Data: 12-mar-2013 17.02
 A: std...@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, std...@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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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 The information in this e-mail is intended only for the person to whom it is
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 HelpLine at
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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

2013-03-20 Thread Anastasia Yendiki


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, std...@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: std...@virgilio.it
Data: 12-mar-2013 17.47
A: ayend...@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: ayend...@nmr.mgh.harvard.edu
Data: 12-mar-2013 17.19
A: std...@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, std...@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: ayend...@nmr.mgh.harvard.edu
 Data: 12-mar-2013 17.02
 A: std...@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, std...@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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