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-XFEDm... https://secure-web.cisco.com/1_MN1cYA-kKEagHaPPlgqZwL_7l1UIz17_aQNq8gtEpI_s2... https://secure-web.cisco.com/1zawiMfJEYesgKKwuXbwTzApr_RjlOcUDaWo3xqmb9Q0qqT... https://secure-web.cisco.com/16BjhjRriW3CRUsbQApyaWMd2fGPbTX5BssSvzhZZyLbnz8...
https://secure-web.cisco.com/18BI4v-eXbN8hzYHtzlbMkSCRqHbcR3o6WbRlxoakoEiyq6... (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.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1pmpbbQ1AtVcPKusWEyZrzTjlUpvhkG62WbQyxcxF1mDyZp... 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-r666u3jM00UuWXUfTXXLF3Iq... 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.