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 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.
