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
[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
