Hi Stefano - Nothing has changed with these variables between 5.1 and 5.2. So do with them whatever you were doing before.
a.y On Thu, 28 Mar 2013, std...@virgilio.it wrote:
Hi Analstasia, as you suggest, adjusting brain mask the tracts are better. Now I'd like to perform trac-all with new version by using a new configuration file. I do not understand what I should do for: 1- set b0mlist 2- set b0plist Thanks. Stefano ----Messaggio originale---- Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 20.22 A: <std...@virgilio.it> Cc: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: Problem with tracula: incomplete or lacking tracts Yes, it's a warning, not an error. On Mon, 25 Mar 2013, std...@virgilio.it wrote: > Hi Anastasia,now I have correct the nodif mask and run again trac-all. > > Is normal "WARN: Could not find satisfactory control point fit - try 83Finding center streamline" during > -prior? > > > Stefano > > > > ----Messaggio originale---- > Da: ayend...@nmr.mgh.harvard.edu > Data: 25-mar-2013 18.02 > A: <std...@virgilio.it> > Cc: <freesurfer@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts > > > I also remember that your brain masks had some big chunks of brain > missing. Was whatever caused that fixed as well? > > On Mon, 25 Mar 2013, std...@virgilio.it wrote: > > > Yes, I fix them. I'm attacking the maps after the last trac-all. > > > > Stefano > > > > > > ----Messaggio originale---- > > Da: ayend...@nmr.mgh.harvard.edu > > Data: 25-mar-2013 17.26 > > A: <std...@virgilio.it> > > Cc: <freesurfer@nmr.mgh.harvard.edu> > > Ogg: Re: 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: <std...@virgilio.it> > > > > Cc: <freesurfer@nmr.mgh.harvard.edu> > > > > 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: <std...@virgilio.it> > > > > > Cc: <freesurfer@nmr.mgh.harvard.edu> > > > > > 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: <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 . 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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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