Hi Samantha - You display a .trk file that was generated in any possible tool,
as long as that tool preserves the image orientation information in the header
of the .trk file. If that info is not there, there is no way for freeview to
guess how to display everything in the same space.
On Apr 13, 2018 3:43 AM, samanthabaldi...@gmail.com wrote:
For our project, we are studying tracts that from two deep brain nuclei spread
to the cortex. Our aim is to find the coordinates of the cortical targets and
compare them across individuals to assess the variability of these projections.
We used the recon-all command for preprocessing of the T1-weighted anatomical
scan and for cortical parcellation. We then switched to the program ExploreDTI,
and we registered the DWI images to the brain.mgz file obtained as output of
recon-all. We performed brain tractography using ROI masks (from fsl atlases)
and obtained tracts files (*.mat, can be converted to *.trk, *.vtk, *.wrl) and
tract masks (*.nii).
Is it possible to import these tract files in Freesurferview? I would like to
obtain one image which shows both the cortical parcellation and the tract of
interest, in order to identify the cortical target based on the labeled model
obtained from Freesurfer.
I first loaded the brain volume brain.mgz (converted to *.nii). Then I selected
“File > Load Tract” (converted to *.trk), but I can only visualize the tract
separately from the brain volume, meaning that it’s not warped into the
I attach a picture of what I obtain.
I wonder whether it is possible to obtain one image as I described above by
importing tracts not obtained with Freesurfer?
Thanks in advance,
Freesurfer mailing list
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.