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
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-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
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
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 AYENDIKI@mgh.harvard.edu wrote:
See "viewing volumes with freeview" in the tutorial: https://secure-web.cisco.com/10RdLE2TlyCn6SHIX3mLEiv_Rt4eMDoWoVQI8x2WCLgHYOa...
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
External Email - Use CautionHi,
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-Cm4n5E1m4dp1UJY3EPioSjfVhLvt... 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_OgzVU0... . 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.
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-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 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 <AYENDIKI@mgh.harvard.edumailto: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_freeviewhttps://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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Sent: Monday, November 22, 2021 5:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://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
freesurfer@nmr.mgh.harvard.edu
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Yendiki, Anastasia -
Zeng, Qi