Hi Emily - Sorry for the confusion. The mask in the bedpostx output directory is a copy of whichever mask was input to bedpostx. By default, tracula uses the anatomical mask for this. If that mask doesn't cover the brain well, I would check for diffusion-to-anatomical miregistration. Probtrackx will use whichever mask you specify as its input.
a.y On Mon, 14 Jul 2014, ebell...@uwm.edu wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
