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://secure-web.cisco.com/11TUQn3ZMjB9gy2mI09erMcLASzJWGpSLFMUxf9tT-XFEDmLfZKdF-O_LIYc_Nlr6rt_zg2mZoh6G-ql4JyDGF9_GKBWGdH3JuQ9aAlzf3dfm7rvxhqKlc2uv5mqmYsc80zjn13a6yKfhlR0WWmUwhZwpGhy5H1vp1y6xKh7DtnYHIGn0HPT11eZFwcabo11doDCbL7I-040PqCDs-uSRWD8uen0ehnSSf9vTMhRoSEsFCjRWI6Bwpj9JUFQtkdyHhOkGLZa0e_LtMmTgeHXhYyBAgp8BZBkCm0NnpqC0vbDOqKNHqNt7xRa7KBZZC34m231hyY_tw-e5GA9WTOZy7Q/https%3A%2F%2Fgithub.com%2Fsrikash%2FMP2RAGE-utils%2Fblob%2Fmain%2Fcore%2Fmp2rage_func%2FRobustCombination.m 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 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 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://secure-web.cisco.com/18BI4v-eXbN8hzYHtzlbMkSCRqHbcR3o6WbRlxoakoEiyq6Y3Fxp9i-3PMN9Ha0O1QFXfqfL4t0D8KxpRCrFEUvpqUWseikOiP-oL_n-uIMVYPoIb9jt6o-tEUQdYtpoNEitW82YuWrsofv06RVCxqIEXYJZL2HZb7AJdhD5JDDeTBfgoiuDpSG6Fkq6DlldSEtub8IhshaapbeMoNd0ZpX4nj_6xo26xhG2SjkGMU-TOKtzrBUZ3-ks_WWCg0_H3ifEPYfxDL2NehLE_iDsUVGWNmBzdTtinfJHzvHOLvt5mmBUTiKQWx0aAzqCh6-5US--T3tJUqER31JXaLZYjtw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fdocs%2Fsynthstrip%2F (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? > > Thanks, > Sara > <slurm-5111070_1.out>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1pmpbbQ1AtVcPKusWEyZrzTjlUpvhkG62WbQyxcxF1mDyZpakHAqzL_nKnR7-dtS6AsA7qJAszQor2PynTQ1SY6BnzpNC9aPmK1BTHVM4K5-KtB7VRxvABZ7G7Kp9HR6dPLUYb3F8kshNlOFqaZKwDJqLAQLuYDf3fqlDJSP3yECIue5H8K0LCMTI7bIKUXE519UsCIrE_0I5De1GfHco-5gCVKs5z9N6LDb3DcvzMZV43NdoETcj8f-gvNnO1STO3tnrz1srzHCX06JYLWCFS2lKhehAc44uIr8LfUUKSt-0BPwWvVeTG6QFwX9E_FPdb0mVijC5k4K23LpiMwMEsA/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/19bDz-6BYKi9Lfy9T-Br5T-r666u3jM00UuWXUfTXXLF3IqAkGdA3e5PYiZPCDBPbfmy2vk0GiN3W8VpAeloIlbP0J1dAUdki1jT9G4kAK1GOYkXWPCUTGiALVG_sxjj2jDaSYNAxatAhrsPIFFaTHAHZEamAZRL6MdyN0iFhkQD0z6vpiGP9fgvPTF9tdqXOn1zTu4jXFoMO6j2shBDDEIOLprVUqm08nPplOj1iODqjgSrdRuz-CRLT3tTiSllbQ9rTZQgIvrFHwuusOYGohhnAbbsuOmTI239QcTPPfYrkj3nTXmNSp-8BHEzTvmuQM5YncEXztf10DuK8m8Tvsg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <https://secure-web.cisco.com/19bDz-6BYKi9Lfy9T-Br5T-r666u3jM00UuWXUfTXXLF3IqAkGdA3e5PYiZPCDBPbfmy2vk0GiN3W8VpAeloIlbP0J1dAUdki1jT9G4kAK1GOYkXWPCUTGiALVG_sxjj2jDaSYNAxatAhrsPIFFaTHAHZEamAZRL6MdyN0iFhkQD0z6vpiGP9fgvPTF9tdqXOn1zTu4jXFoMO6j2shBDDEIOLprVUqm08nPplOj1iODqjgSrdRuz-CRLT3tTiSllbQ9rTZQgIvrFHwuusOYGohhnAbbsuOmTI239QcTPPfYrkj3nTXmNSp-8BHEzTvmuQM5YncEXztf10DuK8m8Tvsg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > 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.
_______________________________________________ Freesurfer mailing list 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. 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
