Hi Jackie - "edgecolor" is not for displaying volumes. It's for displaying surfaces (the outline of each surface that you see in the slice views in those pics). To get the contrast of each volume the way you want it you can play with the sliders under the "Color map" menu.
I recommend that you go through the freeview guide on the wiki, things will make much more sense after that. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide Best, Anastasia. ________________________________ 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 8:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs External Email - Use Caution 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 [FA2.JPG] [RD1.JPG] Thank you! Best, Jackie On Mon, Nov 22, 2021 at 7:27 PM Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@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<https://secure-web.cisco.com/10RdLE2TlyCn6SHIX3mLEiv_Rt4eMDoWoVQI8x2WCLgHYOa_iLiVbEWCPrqo_upK5pKEjdYo4aplg-HRrqRzkfaEU_al0iK2OECP2ZDTv1MdzA-1XnxchLz01JlwyrBgo4ZPonKuAW2xhvQOPWu1liRgGByG2MAoysHLT3mT6QRtCorydcHq0Q5y0XLTF4j0rT1wcrX4MftxWKKCRJi8vgedQAINiadMWOTPdKCll_s7C2Yj0EGncoF91UYoSYejTVTLGEzKLM4KJt_yRRjBZL5E3on8rtcjtgTH7hUKJoyEBlS6bbjht2prEJO4nBWiz/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Zeng, Qi <qi.z...@icahn.mssm.edu<mailto:qi.z...@icahn.mssm.edu>> Sent: Monday, November 22, 2021 5:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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! 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