Anatorig will take you to freesurfer space. I's suggest smoothing these to make them more presentable, and potentially also thresholding them based on the probability map (which is the sum of these streamlines).
On Mon, 7 Mar 2016, Peled, Noam wrote: > I want to display it in my new 3d visualization tool, along the hemispheres > and the subcortical regions. > The hemispheres and the subcortical regions I import from freesurfer. > > Thanks, > Noam > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Monday, March 07, 2016 12:20 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] path.pd.trk format > > What to you want to display it on? If you want to display in on the FA > map, or anything that's in diffusion space, you don't need any transform. > > On Mon, 7 Mar 2016, Peled, Noam wrote: > >> So for plotting the fibers, like in freeview, should I just use the >> <subjid>/dmri/xfms/diff2anatorig.<intra>.mat or >> <subjid>/dmri/xfms/diff2anat.<intra>.mat transformation matrices? >> >> Thanks again, >> Noam >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Monday, March 07, 2016 12:09 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] path.pd.trk format >> >> Yes, native diffusion space. >> >> On Mon, 7 Mar 2016, Peled, Noam wrote: >> >>> Thanks! >>> Do you in which space are the voxel coordinates coordinates? Are they in >>> the diffusion space? >>> >>> Thanks again, >>> Noam >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >>> [ayend...@nmr.mgh.harvard.edu] >>> Sent: Saturday, March 05, 2016 5:10 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] path.pd.trk format >>> >>> Hi Noam - You can read the .trk file with trackvis. It contains all the >>> path samples that are added up to created the probability distribution of >>> the path. Please keep in mind, however, that this .trk file is just meant >>> for generating stats and not for visualization, so these are not the usual >>> smoothed kind of streamlines that you get from deterministic tractography. >>> It contains only integer voxel coordinates, so the streamlines will look >>> sort of like step ladders if you visualize them. >>> >>> Best, >>> >>> a.y >>> >>> On Tue, 16 Feb 2016, Peled, Noam wrote: >>> >>>> Hello, >>>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the >>>> output directory. >>>> How can I read this file? I would like to read the actual splines and not >>>> the probabilistic distribution in path.pd.nii.gz. >>>> >>>> Thanks, >>>> Noam Peled >>>> >>>> >>> _______________________________________________ >>> 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 >> >> >> > _______________________________________________ > 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 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.
