Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts
2 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: > > > > > > Cc: > > > > > > 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: > > > > > > > Cc: > > > > > > > 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: > > > > > > > > Cc: > > > > > > > > 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: > > > > > > > > Cc: > > > > > > > > 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 &g
[Freesurfer] Problem with tracula: incomplete or lacking tracts
.@virgilio.it wrote: > > > > > > > > > > > Here they are attacked. > > > > > > Thanks, > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Messaggio originale > > > > > > Da: ayend...@nmr.mgh.harvard.edu > > > > > > Data: 21-mar-2013 21.50 > > > > > > A: > > > > > > Cc: > > > > > > 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: > > > > > > > Cc: > > > > > > > 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: > > > > > > > > Cc: > > > > > > > > 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: > > > > > > > > Cc: > > > > > > > > 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 > > > &g
Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts
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: > Cc: > 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: > > Cc: > > 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: > > > Cc: > > > 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: > > > > Cc: > > > > 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: > > > > > Cc: > > > > > 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 > >
[Freesurfer] Problem with tracula: incomplete or lacking tracts
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: > Cc: > 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: > > Cc: > > 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: > > > Cc: > > > 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: > > > > Cc: > > > > 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: > > > > > Cc: > > > > > 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 > >
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: Cc: 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: Cc: 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: > Cc: > 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] Problem with tracula: incomplete or lacking tracts
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: Cc: Ogg: [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: Cc: 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: > Cc: > 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.
