[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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Question about Freesurfer
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 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_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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mahdi Babaei < > mahdibabai...@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 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 > https://secure-web.cisco.com/1gadAlf8Jl1436L7J-Mf9mAreqaSz3_sv8nMW4xtyVnUKrG6V0Xiq4wbVxzsGPteEIkCTTOFbzOBaXelmcWYRUTaKKiaoWSJ8QYuAGWCJeKc1fDwKY06wy20_9TtDu_ibY0pRTRVTGVgIpHUWScoQMYoJZc6l8xlpvI7roiaRhy79XwDmmonT_MG0YK8jwGhqjUSUE4KTu17-GdgmCuLtbBIwHbTuUwwjOKDBSldqBgnhRvJ5v-EZItP52LbbncaiJ-wopCvrEpZVg7hl4x8ROBt7RsWfQUS5DUN5Unr3qIAWr6Rx6Pr3suFkhL30-NHfYGi9jFyyyptiSGqANh7vow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Question about Freesurfer
External Email - Use Caution 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 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 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 > 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/1wk8Ikr3bMBJNx4P4Cs2aLd9jcKwjIHfb10mG6VsbIli8adghBnZ8Skcs3IXDCNUMxMI9FYjGTMp1YmOLpAO-gt_QNKQk0UDHD4gfNEwNGh2JLHu3RgbsE2F4F4sXhgjcuEjqBQugowm-awCTkm2fkA2s7WBc_SpOb7yNxnGRolwYtcW5YLw_K-4Ogo-FO13o9m4N3ijk_h_iTDXo1bAC5113a3bc5Aij6EwQjsezVoOAx8lIG-16K50_pgPltPX8n1Kf4vzsplI5rb6uboGsNG0m9pECHFIVD8FPW0EHWWlmh7i2naTYcG5stPgI9K4sz1Xz_1jbsHccMWS-k1UIFw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer >> <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-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mahdi Babaei < >> mahdibabai...@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 >> >> ___ >> 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-wvkkfYoTn8I38sru9aqg2SOUeepILDh644Ik_yrIJl4Q0TCIpM3hObGss3kb_p3SXCrz6JU7qiuUObbKxKymph83fq5JBOtZTq7difd87RROQmffam69krQNEmzIEI1qNYn2XA0_WxSqfjgWBIvaHd3DZ7fe8hKsj2e4dxIa3HU_mZ0A2ShHdcElhX3LziGBIyPXCtd3aGgY44yOB9bQ8N1TkQonlLaLDCGA9aAJuJJ1mxjqe49CmIHxFZ0pfThhJJJyQX2PTqKvqDDpW_qxXdbcuXffr3heSOxVecNp5NFOj0VCcAqJMa94h9xiHw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <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* >> ht
Re: [Freesurfer] Question about Freesurfer
External Email - Use Caution Thank you for the help. It was my bad, I should have changed the Display port to 1. $ export DISPLAY="172.23.144.1:1" Best, Mahdi On Mon, 6 Nov 2023 at 22:31, fsbuild wrote: > Hello Mahdi, > > If you have not already done so, you might want to look at the Freesurfer > wiki notes about setting up an X-server on Windows so linux applications > running in WSL can display graphics using X-windows, > https://secure-web.cisco.com/1mRNN4MVUol3W8CnoB0t_Ukklvy_LWYfeDwOIEfiLfT5jInbyzndn2u3I43Y0kUpVrWqatR_Iz7HmIOLpqqNlSa8iBjH390-X7V2WXCdDnmwd6DIPU0sAm2KnOyjAh2WaWZ96iW1uvNZ9Rbg1r0TygGQ_R2VR7tAIpeS7whHMLXcfNnMs4aOB6mR14agRUIFjtkSDhMMx2rTqEVa2RAics1NQ6vTi0G79Agf8lGFbTlG3uglN4iogRNAmtcSuPsu01GC--CxMoXyavonya_6mwkdAYuEgFKywqvsKaCNS5Fds4j3QONE1F-KT2jxNuBulOVTESu0MerUKSWNKtu9TiQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl > The setup listed > there is for Xming, and you may want to look at both > https://secure-web.cisco.com/1_MFJmdBbOLYbSoW9Ukq5SgcfgA_ZPdkMrakmhniwwoccEftvS6CWHASvY3sG0nH-4kcuSsOpVJv95bi_oOMsGOT1AlVvx6udeItDQwAnwZLm1tJnM_wEsuHXkgSAKR96DA0Ob6Hp92NDiEN21HSG3Fazv6FvuEGF3FJQr-ipoiqKIIpAlJx1-M8MCvdmFyF7vuf_ujPeKq4DKUa3wqmWeuQq7Qrl__gfYaoR6KYqMeXO5u4oH1B1B0i8U81sTVp0ljsUjBpDDxXpQ2G-Xg0PsZlffHGqJuM75VtzNIO_Z8mmX5ow6eQ1_Jg4NAKEs-S3WmS4Yo7Q00gX-9yG6b9XSg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xming > and > https://secure-web.cisco.com/1NdU0BoZky1ppgHOmLBD71xp6n6ZhQMqHqMI3aY_pGKIcdX93N_hgqkDkIKmi7Rb3aRx_ASwwaDShhBcfjUxXez4QFj0gJwE1zrrT68iWALgNLFX3fNsJ48Pow5ZkfX-jCFqV_zKqUurunFpxTI2PARLTRX7NDt13yDR6dTvSxDhVp4lov67CgA6YIoyLNGNrH5JgitLwlwczUfyJ0TrqxdWIUyaFUvZLCLScGTFTlzRI1cDZWZroBAuYiKC-yJvJcDftOvdEPl9_Lbu3SxkkGAdLmzuzPh2hqxcKcvhCP2dPjzlH_k5Oq0v_8NnSA6wmW755LyV92BNLHRMK7COauw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu > > Some people have found Moba X-term, > https://secure-web.cisco.com/1Ed0Br1QC7rO_nMBQtEpcxYqBr3iIXuNBUKsMz0Fpu9biqWb0tZUdTKbfzznCGX9VI_hv-nei9C4H6RpyCJh8_oZA8Ag6FFo8_y1tesQ3QDdeq9GoDj5DN0FAmqJTpKuxGbjGxGNQKWeoLVIwIiaQwFar8THIYPM0nltpnlDGbpHdNoDR4g_Gc-_Ue04ns6_nbj4P8rfeE0uXmBiI1e1OflTVQml-ZN-xmereJXXaJ-z9kramdANndlVyy_heAwnPQJDCuaxSVB48_tEH1JyvsiUeKoyIDoDoqUus-fB0Fh8M2X-CQg_IKrwt3-Xe5DLzbXFXYVwVuUNvkeJ1lNPAhQ/https%3A%2F%2Fmobaxterm.mobatek.net, > easier > to setup and test with glxgears compared to using Xming. > > It’s a good idea to get glxgears to display the spinning gears in an > X-Window before trying to run freeview. Or the display of glxgears can > work, but freeview may still display a black/empty screen. That can be > from the graphics card drivers on the Windows host not being up to date or > not supporting more recent versions of OpenGL. > > There are also quite a few postings about WSL on the freesurfer list. > > - R. > > On Nov 6, 2023, at 13:48, Mahdi Babaei wrote: > > External Email - Use Caution > > 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 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 >> 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 >> 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/1ESe-kTPUKLBexWd97c5IjKvLGFxdGpu_wGcbdl2Q8Oe4-JxivjqTxISm10A1h6BHAjPb_BeiUFnuj6s7_F-oEkE0TyZEO0Am1UZJzmE6Y3NO_4Ywf-C33nKLUVV6g-nY-aE3L-FTo_WDxyt3vbbchN7HcEc4FrX33QIgoyChNlbo3mTK-4VPwj_I5cP1MukkxzSmc6lxnHA1quipf4p4yzT6egQXNTt2elj9q683hcXWxgTA0fjz9G2VHKwfLR-6-2e7ySCWrPupB_5PxHqQ_i2rXg6Vq2ehjDzQd3jwFrxv_qVE2_ow4DpeZahoeEyGXLxgvPu4ltcpll2z3ul0xw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer >>> <https://secure-web.cisco.com/18vNjlLmSGWFTunMb7wArlqA9mQWDmVewpANlk56uM_4t5BjrQ6JC
