Hi Bronwyn Sure, I could take a look, but you might try something like this:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSurfaces?highlight=%28defect%5C_labels%29 first. Look for “defect”. Essentially you can overlay the location and ID of each defect, which if nothing else will tell you that is likely the source of the inaccuracy (or not). Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bronwyn Overs Sent: Sunday, October 13, 2024 11:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Issue with WM surface fill External Email - Use Caution Hi Bruce, Thank you for your reply. On reviewing this participant in Freeview, I'm really not certain if there is a topological defect present, or if the WM and pial surface delineations are incorrect. Would it be possible to send the volume to you for review. If so, how would I go about this? I would greatly appreciate any insight you can provide. Kind regards, Bronwyn Overs Senior Research Assistant [cid:image001.png@01DB1E26.90E5C750] Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 neura.edu.au <http://secure-web.cisco.com/1oacujeZOH_vmWFgondbOK0MDr1E2yb0JCT-OszYYkGEvxvkkcev2iZTFJznpwXBRvk5XDRqnKxd1sFgFxVMc7gW2RrQFfa67x417nJdp2-a69W9bNdDP6oFY7Ix9B8pmaAq5wbP1NYcq6LN-hrhoOY0lK1pFq5ovwNaAc78BPO_Zl_p2aacaS7DBvRhrQVRHl9PLOKd7TT2o7NHBc3RjEUjqBiw-iwxhPti7zHcOV_E6Xx1lqOAfa13GsgJOuD7c9JpGWgy4PEjJIpluHAWGwaBA3OLg-Rdy1Tj9syP4MSOxpMbJypSXndiSym2d2Bb5cv8UOTi0B4SUiyMCMkNYuw/http%3A%2F%2Fneura.edu.au%2F> Twitter<https://secure-web.cisco.com/1YnLCme9b9BpoXBCp5cV8c9Nl7jGsILzont1LaNGaTZAzzBINv4Tc9m6fWo1TTrPqyahVQ7SGEPcUwOWdmBbwKk9sd02XqMnMXdtVFEnBX0_yvN3dbGuX6tNnEMKS6OJ5zuLHb1-_ulvwW1Q3t93pHW1rJ5lLhRS175FVTwYAXbb5qbbPcDSzjbfhzr3tMHRNrjHQ87sWrO0CYpOMEMFLxawwNTrzAnXgMe3f5-Ysnw1f2QWe13mFoJ-YTX3fxTGUqWHWPERQpiv4j17-RJV4Vv4UbAD-9Pxk4vBNQ4--IHLaPvguCGoYobn9nPUb7iaizL95ryvGmhd7aqqbn-jSuw/https%3A%2F%2Ftwitter.com%2Fneuraustralia> | Facebook<https://secure-web.cisco.com/1CP5QM2GwpzEjZlYh_mfA296JyCZ2HEna63ZHYO-qjXsjwfeUsSCX1HpaZMWQnXz5R0XyY2nxLsHsuQSQwsz1ASWJ8G0z2Xf35bPv5MGsYqR9Dn6wNPsU3vUUDJPaBsPbwCNdGIxYE0C6nxDKW2X5pVFgg_kbDfJZY8Wvpa9M9ZfdFcmHqDdhBlkapD2jkroDqXW105QxIvg8xnlDMWLQ0zCCtrklSg4dmsD-RVpagfNcB1Do0eTwLzQ-6LllA75TDV3U9w5IOYY1HKNfWewm7dAKaX2X2TtILO-aAZBC2zEg-kzUPDZlh2Sd6qnCewwT-4kwtY-hsEx6i7vsXBP0kw/https%3A%2F%2Fwww.facebook.com%2FNeuroscienceResearchAustralia> | Subscribe<http://secure-web.cisco.com/19EbfIMdo_6mc8FUC0grTYaxzuT_gdH34C7RbrGgxsuOHXbUizGxeU-zlTFjPNHB21w99xHkprENnz4lrHPIiTaSP9otODgBJC7IZ1MeTNjgTCCR32_J4fOhdG1wMJfS6HOG16WqBflolr9dgz2HAk-9HSqANWuQ9WXVN0nkB6VAXsPlFyQvt9kJxEqWtWHJe4RyxoTx92Llb94crrpXARmL4TMEJaCASK-CYxN47Sfh02wz2mo-O8SXbduGYS2rsoEYd2fE6b2TvzLRqdELyhtSM-S9fegb-jHhD2hRwLGNJkdfceh7A6uh44V4tsLlEdJvx7G9hJgX2yc5dWOwZ_g/http%3A%2F%2Fwww.neura.edu.au%2Fhelp-research%2Fsubscribe> ________________________________ From: "Fischl, Bruce R.,PHD" <bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Sent: Saturday, 12 October, 2024 12:42:03 AM Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Issue with WM surface fill Hi Bronwyn Hard to say without seeing the data, but I would guess that there are topological defects causing these issues. You can overlay the locations of the defects in freeview and see if that explains things. Cheers Bruce 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 Bronwyn Overs Sent: Friday, October 11, 2024 1:31 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Issue with WM surface fill External Email - Use Caution Dear Freesurfer Support, I'm reviewing a specific MRI image that I have processed with Freesurfer V5.3. I'm concerned about a potential issue with voxels missing from the WM surface. This appears to impacting the pial boundaries and lateral ventricle labels in the aseg from slices 56-99. For reference, I attached 5 images (both wm and brainmask surfaces) that are each 5 slices apart. Happy to upload the whole series of images if this would be helpful. Would you recommend filling in some of the voxels near the lateral ventricles? My concern is that I am unsure where the ventricle begins, as I suspect the gyrus at the rh pericalcarine surface is not being properly labelled and identified in the pial surface. Any advice you can provide will be greatly appreciated. Kind regards, Bronwyn Overs Senior Research Assistant [cid:image001.png@01DB1E26.90E5C750] Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 neura.edu.au <http://secure-web.cisco.com/1PhyqjBKyb2oDl07vqwWhBygB_5YJLdeJ41dvzkSKapr3Gum6PQ9n7ClEXO4UGImNUFzfvG-rDbb96NK43FMIFxj7QT1GHRuWqEx06zwUokxt1pDICHuqj1oXpElEAzROVzibpW6q8HwRdv5R5LE34bxeOHUy20Vvoi0-n2lI1Y2f791SVYFo30DjJSs73zDBuajdPd4TK-yDOIdsWhOtpbfoByBg3GnQ62xzFVpC5YeQWQ4uJZzE5NDj0MQC87U58inNXEGC68T0Qcln07Jw2ia3gRnKwMenm_TmdKkccPAMfz_oHPSKfo8VlHCCW8ixwsTPCQ2KPPhx8BG1uLGenw/http%3A%2F%2Fneura.edu.au%2F> Twitter<https://secure-web.cisco.com/1Nq-N5jOYtG9ZB4Dl8PisdSUykSQS1VbMzYkTSuKxvkBDE-5z2p6JsdV6qzDzIquDW13vGrAevKG-SvYnmlowIUSVwzZ6KUp3IaJlzVsacdzHnHPuN3QNqRl0qLoxttZjALO4noUZijGCYL15EGnuJ647GdEj9aRy7KBFGS4KaO9ZAsw5qLF1YimRNcx2lTNy9VhFcRUpamATi2eptyHtG5XfSEMiIWivopt6hiS4CwCO-MBpnWGkDMCz1lzfZAvQCBLSGkOXKpXWMPMc_0_NiX3fJ6OZEkv4nLFl5Wo_zucvgf4uOuX1PJWp9Zm4NXhu6akkvfqyGqqfxMiRLQmf7g/https%3A%2F%2Ftwitter.com%2Fneuraustralia> | Facebook<https://secure-web.cisco.com/1wYi0bZZPKh6dadEH9ixKmgt3NP7bvL1I_HLfiwg9s6h5-rQsKbmf9iSJLfHjAHmLRVuKFwhXPF9zW8XvY__CD58RmyL5O0lW1E-_jmJIBqLewS-rxSQ_jJna4wS7gZPkPfn7ydUBZcSPQ6wzEQy4PGD6ThKERhWXDWs-x_ZsL1Z8Yt0JY-X7XHvA-Vv-CH5PWvkuCTk_h_pY9biBVFLpoaImsXSvP6a51uZml7cQbaVSUjQhSOCPTABCRi559bOUGa2uvXRUqRaYlK1zhMqf_DY7pguNCm0eUt_G2HVPfNN1HzQNhNhYgehT4rQYUVlRwz6aEvm8NRBL-r6229wg0Q/https%3A%2F%2Fwww.facebook.com%2FNeuroscienceResearchAustralia> | Subscribe<http://secure-web.cisco.com/1yUpg4OTzIo3qIvjsCh2VZmcvRXG4uvBgKotJ3qtYmng5K2GBPLCsd1Nebu2CwmvcKOi4--Wjai-jT56KJEQWIr2p0t57q3a5_L-Tnb2rwV_GrUKLeEWqFcIRRKRJJHqc6t8v-zA4Ao4HU2bPVHw5JF0nFGxp_wVZ4EOVL8sSy8M5H_A9nyeSZg8_wlBzcJt69TdK_PEh1qIyFHy73y7G9To8UXC2DEsE6R-nUEJZhzYbrvMSBRzCPE6bzWjExIuBcWImcjJpm31R94YhR1_kIRciFQnUfOHLOxI_umCBQOMoDlfn-6Zn_eni1biBBIIIV-12jkNRXbRs0A_6XkQM6Q/http%3A%2F%2Fwww.neura.edu.au%2Fhelp-research%2Fsubscribe> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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