Thank you all for the help. I have available the T1 post contrast, could I use it alternatively? (After freesurfer analysis I have to do tracula analysis).
Thanks, Sara Inviato da Outlook per iOS<https://aka.ms/o0ukef> ________________________________ Da: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> per conto di Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu> Inviato: Sunday, September 29, 2024 4:20:00 AM A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error You could try synthstrip, it might work Cheers Bruce On Sep 29, 2024, at 7:38 AM, William Baare <w...@drcmr.dk> wrote: External Email - Use Caution Hi Sara, You need to denoise the background. Here are some links that might be of help. Always check the quality of the output :-) https://github.com/srikash/MP2RAGE-utils/blob/main/core/mp2rage_func/RobustCombination.m MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/JosePMarques/MP2RAGE-related-scripts<https://secure-web.cisco.com/1_MN1cYA-kKEagHaPPlgqZwL_7l1UIz17_aQNq8gtEpI_s21m5q0Dk-NNA1GpJ0qz9MZylJZTxfNcdHX6oB-Rd6NTRfG9Y7jvYF3YzCZLUOYKgXKYMLpRYsrx2wWUK_cjaAiqIhc881eAujRSsciwbSOrxXuehaPX0gLR7hc9oyJZVj9RI85MzrVJz-duGY0dL9vGepgc2rq7jO6cdYUeO6clS9WxY9Dvs0N_9RQGWPPYnX0etEEV-ON5j0NWWAxlVwBD_JhtBGwUGOhfVZsS_yoKAxKl_pyMOywN1q18lMvKjUNSGqxqBPNYszM0E0D1rn-06aymELBVZfXQvQ1Y4g/https%3A%2F%2Fgithub.com%2FJosePMarques%2FMP2RAGE-related-scripts> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/srikash/presurfer?tab=readme-ov-file<https://secure-web.cisco.com/1zawiMfJEYesgKKwuXbwTzApr_RjlOcUDaWo3xqmb9Q0qqTasKaAlNOngj40ZYQOPj1lps9A4U4IntfCY1H_dCm9_uvGl7FwRP_hXSywB_PIEVdsnxY3PmSiPodCYxMIvbfOP3kwl3CRf3U98UsZdhtf2AZ9FzSs4inSytMusfZZa9UuDR9pjtnCY0TABMZq5bUXv_e_QLuh0zURQ_TkWX3ZnXeSlDGEM5z7q1BbbDnIN75GsqHOvkNWKFpywV9SnRE7a-X3lxrO1dSfD34CTW9y1Ei4FjRpxqi_u89IM_xSQ7lSpO0o6pTMIUWDxpXb1q7mujDwj04A_W37-73k0sA/https%3A%2F%2Fgithub.com%2Fsrikash%2Fpresurfer%3Ftab%3Dreadme-ov-file> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/srikash/3dMPRAGEise<https://secure-web.cisco.com/16BjhjRriW3CRUsbQApyaWMd2fGPbTX5BssSvzhZZyLbnz8_i4PtLRN5QiZUcz7HQ_uei4EmIroeeBnKGIQxmbI6rI-oWfDmO-sexqor-PvDOj0L9wt1gJcipUPnylZtByZKt_dmEbcfENd5Km6WN9dia3cv5AVbhCRmMagEiz_CMGS2hSdZ3VTzyvZ-E-qId7CEFs4yGgxvSVv8Xv7PNjMj2-DlRTDQpM8DpyDYwxmSoIbjxuXX2rkXi3yCDAi0p-vPHVkef_ki37h51GAFsaB6grbd8raSV3wwMkBePUtw_HHkOyDRFN5qnCDI_GSVXiz7faKdJuKEuyU-jLwbADA/https%3A%2F%2Fgithub.com%2Fsrikash%2F3dMPRAGEise> https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/ (incorporated in freesurfer) Cheers William On 28 Sep 2024, at 18.27, De Giorgi, Sara <sdegio...@mgh.harvard.edu> wrote: Dear all, Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only sequence we have. This is how it looks: <image.png> This is how the skull stripping appears: <image.png> Please find the log file as an attachment. I also tried to manually adjust brainmask.mgz , but also brain.mgz is incorrect. How can I solve this issue? 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