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 [image: FA2.JPG] [image: RD1.JPG] Thank you! Best, Jackie On Mon, Nov 22, 2021 at 7:27 PM Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote: > See "viewing volumes with freeview" in the tutorial: > 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 < > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1wqxCmEbMWS5bXmDde-Cm4n5E1m4dp1UJY3EPioSjfVhLvtmmhseHGrij0l9P_Hn3izt3ymdMTSFSQpZQ2imRnd2IuZ_y0JeXVKtxZuDm6o0YgKjhdItPeYzIARWba5Dpkb8TbT0DDiMcxgLMxaREMKon6ZC8sM6xJFjVyxBzoZeuvUtOp_Pqy26n8C4RSdSIUn6wAyqpAuSi1pqeZeIy1S1VhBEHfKiII6_PdjXsigzC4qWBtceVe11PlzNVhNBPvywYtVtG_f_huc5oHGVw2xib2ey5LA_zGkZISloTRVtLCwHB7VA0VoL8NvOIEHxH/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/1ZwvmXrSa5vi0hTZk0ZMYKm8seFVH4b6-ZuTUhJtG_OgzVU0T6Ep_5EsvDC74NVufQASXmbxe5a9H5wLz6qKK8n7WX2hcBpt9jShg01Ld31LLtFfFN1YVoR8RYErVUiQ0rE33PNLOiqDEcMTDHEmnw0DV-pvIoAi0yXIExdo6TRL95Xaz8bjUn_su4pDRKBUKSaoMehVwsUaio7PfxdvJuGK2tsIdQYZWTONwJSO2Kf3wEmuf_WyokG5H7EV_qX-ynOXISVSMaUDWibIrpnE_u8zRTsnzywkc6Yco4vCW0bStbivPbF7E7NkQHnHsgkkg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > -- Ph.D. candidate Icahn School of Medicine at Mount Sinai
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