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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayendiki@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayendiki@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
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