Hi Anastasia, So probtractx uses the output from the bedpost stage (which I ran in Tracula). I noticed that the bedpost stage (in the dmri.bedpostx folder) also outputs a no_dif_brain mask. I guess what I am worried about is that if bedpost creates this no_dif_brain mask, that is what will be utilized in probtractx instead of the Freesurfer brain mask.
When bedpost is conducted in Tracula, is the brain mask from the freesurfer segmentation of the structural scan utilized? I am sorry. I know I am making this confusing! Thanks, Emily ----- Original Message ----- From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, July 14, 2014 10:18:11 AM Subject: Re: [Freesurfer] Tracula Hi Emily - When a mask is used as input to bedpostx, all voxels outside that mask will be zero in all bedpostx output volumes. So it makes sense to use the same mask for any subsequent processing. Is the mask that you're referring to a symbolic link to another volume? You can run ls -l to see what volume it points to. a.y On Mon, 14 Jul 2014, ebell...@uwm.edu wrote: > Hi Anastasia, > > Thank you so much, this is really helpful. > > I have one other question. So, at the bedpost stage, the no_dif_brain mask is > used correct (looking at the fsl webpage), or at this stage the freesurfer > segmentation is used as well? > > If in addition to using tracula, lets say if I also wanted to look into doing > local probablistic tractography in FSL (using probtractx). I know that > probtractx uses the output from the fsl bedpost stage. In this case then, > would I need to adjust the no_dif_brain mask since it was used in the bedpost > stage? I planned on using the output from the bedpost stage in tracula into > FSL's probtractx to also try some local probablistic tractography. > > Emily > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Sent: Monday, July 14, 2014 4:14:49 AM > Subject: Re: [Freesurfer] Tracula > > > Hi Emily, > > 1. That's fine because the BET-based mask is not used by default in the > the tractography. The brain mask from the freesurfer segmentation of the > structural scan is used instead. > > 2. To check the diffusion-to-anatomical registration, you can look at the > aparc+aseg registered into diffusion space, i.e., from the dlabel/diff > directory, overlaid onto the FA map. It's also important to check that the > gradient table is correct by looking at dtifit_V1 (the primary eigenvector > of the tensors) displayed as lines. Assuming the protocol is the same for > all subjects, you just need to do this latter check for one of your > subjects only. > > 3. TRACULA doesn't do whole-brain tractography. It reconstructs a set of > specific tracts. Information on the anatomical regions that these tracts > go through or next to is derived from a set of training subjects. See our > paper for more info: > > http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract > > Hope this helps, > a.y > > On Thu, 10 Jul 2014, ebell...@uwm.edu wrote: > >> Hello, >> >> I have a few questions about Tracula. I am very new to DTI, so I hope you >> can bare with me. >> >> 1.) I have been checking my registration at the prep stage. I am very new to >> this so it may be that I am not looking at the right files. >> >> I looked at my eddy current corrected diffusion data (which I believe is in >> data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed >> that the no_dif_brain_mask does not cover very well for some of my subjects. >> Should I individually tailor the Fractional Intensity Threshold for BET mask >> extraction from low-b images at the prep stage? >> >> >> 2.) In general what files should I be checking at each phase (prep, bedpost, >> path)? >> >> 3.)How do you generate the whole-brain ROIS to guide the tractography (is >> the white matter mask that is generated at the prep phase involved)? >> >> Thanks, >> >> Emily >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
