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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