Thanks a lot for the advice!!. One thing that is still not clear to me: at which freesurfer step do you use synthstrip (or the manual version)? I am trying to run autorecon1 and then swap the brainmask but then autorecon2 fails.
Best, 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 Joshua K Lee <jki...@ucdavis.edu> Inviato: Sunday, September 29, 2024 5:53:01 PM A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error External Email - Use Caution I just want to add (from out of nowhere) that synthstrip is fantastic..highly reliable and accurate. Josh Lee Assistant Professional Researcher Department of Psychiatry and Behavioral Sciences University of California, MIND Institute jki...@ucdavis.edu ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu> Sent: Sunday, September 29, 2024 1:20 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: 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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