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 iOShttps://aka.ms/o0ukef ________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Joshua K Lee jkilee@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
jkilee@ucdavis.edu
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@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 wimb@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/RobustC... MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/JosePMarques/MP2RAGE-related-scriptshttps://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-filehttps://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/3dMPRAGEisehttps://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 sdegiorgi@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.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/19bDz-6BYKi9Lfy9T-Br5T-r666u3jM00UuWXUfTXXLF3IqAkGdA3e5PYiZPCDBPbfmy2vk0GiN3W8VpAeloIlbP0J1dAUdki1jT9G4kAK1GOYkXWPCUTGiALVG_sxjj2jDaSYNAxatAhrsPIFFaTHAHZEamAZRL6MdyN0iFhkQD0z6vpiGP9fgvPTF9tdqXOn1zTu4jXFoMO6j2shBDDEIOLprVUqm08nPplOj1iODqjgSrdRuz-CRLT3tTiSllbQ9rTZQgIvrFHwuusOYGohhnAbbsuOmTI239QcTPPfYrkj3nTXmNSp-8BHEzTvmuQM5YncEXztf10DuK8m8Tvsg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://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