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.
