See "viewing volumes with freeview" in the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview
When you view the aseg, aparc+aseg, or any other FreeSurfer segmentation
volume, make sure that the colormap is not grayscale but "look-up table".
You can get the AD and RD from the other outputs:
AD = L1
RD = (L2+L3)/2
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi
<qi.z...@icahn.mssm.edu>
Sent: Monday, November 22, 2021 5:24 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freeview grey matter, white matter and Tracula outputs
External Email - Use Caution
Hi,
If I want to freeview fully segmented grey matter, white matter, and Tracula
outputs, are the following commands correct to the request?
# to visualize the segmented cortical outputs
freeview -v mri/aparc+aseg.mgz
Question: why is one hemisphere brighter than the other? How can I adjust so
that they are equally bright?
# to visualize the segmented subcortical outputs
freeview -v mri/aseg.mgz
Question: why is only one hemisphere showing and how to add the other one?
$ to visualize AD. RD, FA and color-coded each
freeview -v dmri/dtifit_FA.nii
Question: I cannot find the nifti outputs of AD and RD (however, the stats
generated). where can I find it? Is there an example of how to color-code them
for freeview?
Thank you!
Best,
Jackie
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