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.
Best, a.y
On Apr 13, 2018 3:43 AM, samanthabaldi145@gmail.com wrote: Good morning,
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 subject’s brain. 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, Regards
Samantha Baldi