Hi Anastasia,

I tried to visualize the RD.nii with the following steps, however, it doesn't represent well as fa.nii does. (attached below).

1) RD = (L2+L3)/2: fslmaths dtifit_L2.nii -add dtifit_L3 -div 2 dtifit_RD.nii

2) mri_vol2vol --mov dmri/lowb.nii --targ mri/wmparc.mgz --inv --interp nearest --o mri/wmparc2diff.mgz --reg dmri/xfms/anatorig2diff.bbr.dat --no-save-reg

3) mri_mask dmri/dtifit_RD.nii mri/wmparc2diff.mgz dmri/rd-masked.mgz

4) freeview -v dmri/dtifit_RD.nii dmri/rd-masked.mgz

If I tried to color-code every diffusivity (rd, ad, fa), I failed by adding "edgecolor=red(blue, or yellow)" following, what are the other options?

>> freeview -v dmri/dtifit_FA.nii:reg=dmri/xfms/anatorig2diff.bbr.dat:edgecolor=red dmri/dtifit_AD.nii:reg=dmri/xfms/anatorig2diff.bbr.dat:edgecolor=yellow...

FA.nii RD.nii

Thank you!

Best,

Jackie

On Mon, Nov 22, 2021 at 7:27 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

See "viewing volumes with freeview" in the tutorial:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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-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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