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Dear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New Jersey, USA, where my research focuses on MRI to PET translation. I have a number of problems. Freeview opens fine but when I load a column in it just shows a black view. Have you ever encountered this problem? I'm so confused about using the tool for registration. Can I do registration between MRI and PET modalities of the same subject using " bbregister"?
Best, Mahdi
Hi Mahdi,
I'm afraid I don't know what you mean by "Freeview opens fine but when I load a column in it just shows a black view." What is a column in this context?
As for registration between PET and MR, have you seen this page? https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
It suggests using mri_coreg.
-Paul
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mahdi Babaei mahdibabaii45@gmail.com Sent: Sunday, November 5, 2023 2:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Question about Freesurfer
External Email - Use Caution
Dear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New Jersey, USA, where my research focuses on MRI to PET translation. I have a number of problems. Freeview opens fine but when I load a column in it just shows a black view. Have you ever encountered this problem? I'm so confused about using the tool for registration. Can I do registration between MRI and PET modalities of the same subject using "bbregister"?
Best, Mahdi
External Email - Use Caution
Hi Paul,
Thank you for your response. There was an issue with my description. I meant to refer to volume data. Freeview is displaying a black view, even though it loads the images. Unfortunately, nothing is visible.
Best, Mahdi
On Mon, 6 Nov 2023 at 11:30, Wighton, Paul PWIGHTON@mgh.harvard.edu wrote:
Hi Mahdi,
I'm afraid I don't know what you mean by "Freeview opens fine but when I load a column in it just shows a black view." What is a column in this context?
As for registration between PET and MR, have you seen this page? https://secure-web.cisco.com/18vNjlLmSGWFTunMb7wArlqA9mQWDmVewpANlk56uM_4t5B...
It suggests using mri_coreg.
-Paul
From: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mahdi Babaei < mahdibabaii45@gmail.com> Sent: Sunday, November 5, 2023 2:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Question about Freesurfer
External Email - Use CautionDear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New Jersey, USA, where my research focuses on MRI to PET translation. I have a number of problems. Freeview opens fine but when I load a column in it just shows a black view. Have you ever encountered this problem? I'm so confused about using the tool for registration. Can I do registration between MRI and PET modalities of the same subject using "bbregister"?
Best, Mahdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1CXTsUV37CfUTW3oZRJvaO2BxHul7xKuFDYfv1wThzJ5IE6... 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 https://secure-web.cisco.com/1gadAlf8Jl1436L7J-Mf9mAreqaSz3_sv8nMW4xtyVnUKrG... < https://secure-web.cisco.com/1gadAlf8Jl1436L7J-Mf9mAreqaSz3_sv8nMW4xtyVnUKrG... .
It sounds like an openGL rendering issue. If you run glxgears command, do you see a blank window or spinning 3D gears?
Ruopeng
On Nov 6, 2023, at 12:37 PM, Mahdi Babaei <mahdibabaii45@gmail.commailto:mahdibabaii45@gmail.com> wrote:
External Email - Use Caution
Hi Paul,
Thank you for your response. There was an issue with my description. I meant to refer to volume data. Freeview is displaying a black view, even though it loads the images. Unfortunately, nothing is visible.
Best, Mahdi
On Mon, 6 Nov 2023 at 11:30, Wighton, Paul <PWIGHTON@mgh.harvard.edumailto:PWIGHTON@mgh.harvard.edu> wrote: Hi Mahdi,
I'm afraid I don't know what you mean by "Freeview opens fine but when I load a column in it just shows a black view." What is a column in this context?
As for registration between PET and MR, have you seen this page? MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurferhttps://secure-web.cisco.com/18vNjlLmSGWFTunMb7wArlqA9mQWDmVewpANlk56uM_4t5BjrQ6JC20xM-IfCGjRTVm8JHBTAKDDjGTfWTlR0Tl7pWwpQDTa9iUq5xuXmzq5FhvZYz4CougtZUc0KSwUghDHRf5GSNhe450T_mfdBXXqZEagt2weB4ir46dEC1DQpQ8FV7PEIuiLy1z3HVp3gbjCsii3j4j03rTzmmPs5FUP-VmkbKWIa7_dLCtbBDJidWYD2UEyV7ab5r6eKb0byoeD5Qd53y4Iok2NVwnUXajXd4ZCe1R8wQt8Ndoe2_mSWLSLu8ae6eDQHoXaJeC_iT1Z1F4-j4b4v9uBN0Fdvvw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
It suggests using mri_coreg.
-Paul
________________________________________ 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 Mahdi Babaei <mahdibabaii45@gmail.commailto:mahdibabaii45@gmail.com> Sent: Sunday, November 5, 2023 2:25 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Question about Freesurfer
External Email - Use Caution
Dear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New Jersey, USA, where my research focuses on MRI to PET translation. I have a number of problems. Freeview opens fine but when I load a column in it just shows a black view. Have you ever encountered this problem? I'm so confused about using the tool for registration. Can I do registration between MRI and PET modalities of the same subject using "bbregister"?
Best, Mahdi
_______________________________________________ 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/1CXTsUV37CfUTW3oZRJvaO2BxHul7xKuFDYfv1wThzJ5IE6-V0mBDybd5X-iACaRakRLqQWtXSWV7U-0yNNHC35tE8jr8dHUvvmUPD0XPkcZ7LDdw_yHZw3HPMWivcGoVRmhI49jWjUJF1R10aaTZ74is17hRMQVLNIdbQXFF2AF_8ue2meHzN4zsY9AQRD5BVH3xuuRMvXAgrJARilJrtAHqn_4NpFr1vTFQbAmXmNcz6WF6blITCF2KECL8Yh5NeBsIPi9toUhOT2u3p_UGVMuV9QQ80r_Zv3DKOoa8ujEprUUjbRuBsVtChqOLblstnrFJmX2ghJWA5PKB4RLx7Q/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 https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gadAlf8Jl1436L7J-Mf9mAreqaSz3_sv8nMW4xtyVnUKrG6V0Xiq4wbVxzsGPteEIkCTTOFbzOBaXelmcWYRUTaKKiaoWSJ8QYuAGWCJeKc1fDwKY06wy20_9TtDu_ibY0pRTRVTGVgIpHUWScoQMYoJZc6l8xlpvI7roiaRhy79XwDmmonT_MG0YK8jwGhqjUSUE4KTu17-GdgmCuLtbBIwHbTuUwwjOKDBSldqBgnhRvJ5v-EZItP52LbbncaiJ-wopCvrEpZVg7hl4x8ROBt7RsWfQUS5DUN5Unr3qIAWr6Rx6Pr3suFkhL30-NHfYGi9jFyyyptiSGqANh7vow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gadAlf8Jl1436L7J-Mf9mAreqaSz3_sv8nMW4xtyVnUKrG6V0Xiq4wbVxzsGPteEIkCTTOFbzOBaXelmcWYRUTaKKiaoWSJ8QYuAGWCJeKc1fDwKY06wy20_9TtDu_ibY0pRTRVTGVgIpHUWScoQMYoJZc6l8xlpvI7roiaRhy79XwDmmonT_MG0YK8jwGhqjUSUE4KTu17-GdgmCuLtbBIwHbTuUwwjOKDBSldqBgnhRvJ5v-EZItP52LbbncaiJ-wopCvrEpZVg7hl4x8ROBt7RsWfQUS5DUN5Unr3qIAWr6Rx6Pr3suFkhL30-NHfYGi9jFyyyptiSGqANh7vow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks for the reply. Yes, glxgears command shows a blank window. I thought about it but couldn't find any solution. I'm working on WSL2.
Best, Mahdi
On Mon, 6 Nov 2023 at 13:16, Wang, Ruopeng RWANG4@mgh.harvard.edu wrote:
It sounds like an openGL rendering issue. If you run glxgears command, do you see a blank window or spinning 3D gears?
Ruopeng
On Nov 6, 2023, at 12:37 PM, Mahdi Babaei mahdibabaii45@gmail.com wrote:
External Email - Use CautionHi Paul,
Thank you for your response. There was an issue with my description. I meant to refer to volume data. Freeview is displaying a black view, even though it loads the images. Unfortunately, nothing is visible.
Best, Mahdi
On Mon, 6 Nov 2023 at 11:30, Wighton, Paul PWIGHTON@mgh.harvard.edu wrote:
Hi Mahdi,
I'm afraid I don't know what you mean by "Freeview opens fine but when I load a column in it just shows a black view." What is a column in this context?
As for registration between PET and MR, have you seen this page? *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wk8Ikr3bMBJNx4P4Cs2aLd9jcKwjIHfb10mG6VsbIli8ad... https://secure-web.cisco.com/18vNjlLmSGWFTunMb7wArlqA9mQWDmVewpANlk56uM_4t5BjrQ6JC20xM-IfCGjRTVm8JHBTAKDDjGTfWTlR0Tl7pWwpQDTa9iUq5xuXmzq5FhvZYz4CougtZUc0KSwUghDHRf5GSNhe450T_mfdBXXqZEagt2weB4ir46dEC1DQpQ8FV7PEIuiLy1z3HVp3gbjCsii3j4j03rTzmmPs5FUP-VmkbKWIa7_dLCtbBDJidWYD2UEyV7ab5r6eKb0byoeD5Qd53y4Iok2NVwnUXajXd4ZCe1R8wQt8Ndoe2_mSWLSLu8ae6eDQHoXaJeC_iT1Z1F4-j4b4v9uBN0Fdvvw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
It suggests using mri_coreg.
-Paul
From: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mahdi Babaei < mahdibabaii45@gmail.com> Sent: Sunday, November 5, 2023 2:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Question about Freesurfer
External Email - Use CautionDear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New Jersey, USA, where my research focuses on MRI to PET translation. I have a number of problems. Freeview opens fine but when I load a column in it just shows a black view. Have you ever encountered this problem? I'm so confused about using the tool for registration. Can I do registration between MRI and PET modalities of the same subject using "bbregister"?
Best, Mahdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1doY5zuW1fTHCRmXqhLHXkhe-wvkkfYoTn8I38sru9aqg2S... https://secure-web.cisco.com/1CXTsUV37CfUTW3oZRJvaO2BxHul7xKuFDYfv1wThzJ5IE6-V0mBDybd5X-iACaRakRLqQWtXSWV7U-0yNNHC35tE8jr8dHUvvmUPD0XPkcZ7LDdw_yHZw3HPMWivcGoVRmhI49jWjUJF1R10aaTZ74is17hRMQVLNIdbQXFF2AF_8ue2meHzN4zsY9AQRD5BVH3xuuRMvXAgrJARilJrtAHqn_4NpFr1vTFQbAmXmNcz6WF6blITCF2KECL8Yh5NeBsIPi9toUhOT2u3p_UGVMuV9QQ80r_Zv3DKOoa8ujEprUUjbRuBsVtChqOLblstnrFJmX2ghJWA5PKB4RLx7Q/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* https://secure-web.cisco.com/1jPSoSn8N7r_A7EDQuCX7ogucX914Vg9LM6cKRAgbxA-2K2... https://secure-web.cisco.com/1gadAlf8Jl1436L7J-Mf9mAreqaSz3_sv8nMW4xtyVnUKrG6V0Xiq4wbVxzsGPteEIkCTTOFbzOBaXelmcWYRUTaKKiaoWSJ8QYuAGWCJeKc1fDwKY06wy20_9TtDu_ibY0pRTRVTGVgIpHUWScoQMYoJZc6l8xlpvI7roiaRhy79XwDmmonT_MG0YK8jwGhqjUSUE4KTu17-GdgmCuLtbBIwHbTuUwwjOKDBSldqBgnhRvJ5v-EZItP52LbbncaiJ-wopCvrEpZVg7hl4x8ROBt7RsWfQUS5DUN5Unr3qIAWr6Rx6Pr3suFkhL30-NHfYGi9jFyyyptiSGqANh7vow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1jPSoSn8N7r_A7EDQuCX7ogucX914Vg9LM6cKRAgbxA-2K2... https://secure-web.cisco.com/1gadAlf8Jl1436L7J-Mf9mAreqaSz3_sv8nMW4xtyVnUKrG6V0Xiq4wbVxzsGPteEIkCTTOFbzOBaXelmcWYRUTaKKiaoWSJ8QYuAGWCJeKc1fDwKY06wy20_9TtDu_ibY0pRTRVTGVgIpHUWScoQMYoJZc6l8xlpvI7roiaRhy79XwDmmonT_MG0YK8jwGhqjUSUE4KTu17-GdgmCuLtbBIwHbTuUwwjOKDBSldqBgnhRvJ5v-EZItP52LbbncaiJ-wopCvrEpZVg7hl4x8ROBt7RsWfQUS5DUN5Unr3qIAWr6Rx6Pr3suFkhL30-NHfYGi9jFyyyptiSGqANh7vow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1doY5zuW1fTHCRmXqhLHXkhe-wvkkfYoTn8I38sru9aqg2S... 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 https://secure-web.cisco.com/1jPSoSn8N7r_A7EDQuCX7ogucX914Vg9LM6cKRAgbxA-2K2... < https://secure-web.cisco.com/1jPSoSn8N7r_A7EDQuCX7ogucX914Vg9LM6cKRAgbxA-2K2... .
freesurfer@nmr.mgh.harvard.edu
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Mahdi Babaei -
Wang, Ruopeng -
Wighton, Paul