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 > > > 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 . 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 . 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 . 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 . 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.
