See "viewing volumes with freeview" in the tutorial:

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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

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@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

 

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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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