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 > > > which is the possible error. > > > > > > > > > Stefano > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > 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 > > 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. > > > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 > 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 . 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