Dear all,
Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only sequence we have. This is how it looks: [cid:22ca1ab1-56b5-42b4-a482-23e883ecfab5]
This is how the skull stripping appears:
[cid:b3faf493-9947-4d50-a296-1f0456d5382d]
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
External Email - Use Caution
Hi Sara,
If you happen to also have INV1 and INV2, one solution is to run mri_synthstrip on any of these two images (instead of on UNI) and save the brain mask using option -m. This should give you a better brain mask since the background of INV1 and INV2 are not as noisy as UNI. Once you have the brain mask, you can just multiply the brain mask by UNI.
Best, Kaibo ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of De Giorgi, Sara sdegiorgi@mgh.harvard.edu Sent: Saturday, September 28, 2024 12:27 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer - skull stripping error
You don't often get email from sdegiorgi@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1Qi9-mzX54zbfj2NYyLY8UQ1EQ0t7O2DFNIa42-TxWzbKGzEP4GgmOgsj5MFao5nzV8Pg4EqZG9aAJI1o-t9jwxXo6lbcBwLS8qofF7_VJrViMFWR8-59tsQIH8a3r5rirKZkb8bq6SsY5m9gebK8tkkzw8mf276VhDf3dngbOFQ39vdHTn5qODxxhnOGAOhls_OQaEJ-xA_nre_unYDSWOgxL1x9oe0tXs_S798XBG6CKRr76d8ivywSY2Gc-PKNEjZsbhhX5dKD8dyEJXMSx36ZU1jHmvVsQlV0bkzs5VdXNRH_6tLZzU-mJxkDNl8Tg4vYwbIGrWczyZphGSJlmQ/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Dear all,
Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only sequence we have. This is how it looks: [cid:22ca1ab1-56b5-42b4-a482-23e883ecfab5]
This is how the skull stripping appears:
[cid:b3faf493-9947-4d50-a296-1f0456d5382d]
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
Thank you for your reply. Unfortunately, I have only UNI.
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 Tang, Kaibo ktang@unc.edu Inviato: Saturday, September 28, 2024 3:57:23 PM A: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error
External Email - Use Caution
Hi Sara,
If you happen to also have INV1 and INV2, one solution is to run mri_synthstrip on any of these two images (instead of on UNI) and save the brain mask using option -m. This should give you a better brain mask since the background of INV1 and INV2 are not as noisy as UNI. Once you have the brain mask, you can just multiply the brain mask by UNI.
Best, Kaibo ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of De Giorgi, Sara sdegiorgi@mgh.harvard.edu Sent: Saturday, September 28, 2024 12:27 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer - skull stripping error
You don't often get email from sdegiorgi@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1Qi9-mzX54zbfj2NYyLY8UQ1EQ0t7O2DFNIa42-TxWzbKGzEP4GgmOgsj5MFao5nzV8Pg4EqZG9aAJI1o-t9jwxXo6lbcBwLS8qofF7_VJrViMFWR8-59tsQIH8a3r5rirKZkb8bq6SsY5m9gebK8tkkzw8mf276VhDf3dngbOFQ39vdHTn5qODxxhnOGAOhls_OQaEJ-xA_nre_unYDSWOgxL1x9oe0tXs_S798XBG6CKRr76d8ivywSY2Gc-PKNEjZsbhhX5dKD8dyEJXMSx36ZU1jHmvVsQlV0bkzs5VdXNRH_6tLZzU-mJxkDNl8Tg4vYwbIGrWczyZphGSJlmQ/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Dear all,
Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only sequence we have. This is how it looks: [cid:22ca1ab1-56b5-42b4-a482-23e883ecfab5]
This is how the skull stripping appears:
[cid:b3faf493-9947-4d50-a296-1f0456d5382d]
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
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.
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
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 iOShttps://aka.ms/o0ukef ________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Fischl, Bruce R.,PHD BFISCHL@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 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
Synthstrip is extremely robust, it on both Cheers Bruce
On Sep 29, 2024, at 6:34 PM, De Giorgi, Sara sdegiorgi@mgh.harvard.edu wrote:
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 iOShttps://aka.ms/o0ukef ________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Fischl, Bruce R.,PHD BFISCHL@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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://secure-web.cisco.com/1dRuxSA4h9rnOhMJRNBEr790phW8LKhre1MLsJpnnS0gxWo... MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/12o4BSWiv1iyZ9W75913--OTv9wW-0Q0ALCAKS4gbOZanZw...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://secure-web.cisco.com/1rL_7sYD8lxpRfTZff-qlE1A1u-t9Q3ZJ6hiNEQQ-Tmdj8z...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://secure-web.cisco.com/1XzJUV7lKcqMQVqsW1M6EYAema7W2JV5v2NdBGmgyTqFSF2...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/1szgS5ncRMmXYiE0It-GuxwpXSrOs91SjsE1o1Tpq4vOpTI... (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://secure-web.cisco.com/1R2xAoG-4D6Lo_1SB4QZ2cfxYjmIuCIrFEf64VhtY3cC05o...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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1g9Fv6v12-SlBXEvPHTLOiM89YeX56YKpcziKNy6BC0SKph...https://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://secure-web.cisco.com/1g9Fv6v12-SlBXEvPHTLOiM89YeX56YKpcziKNy6BC0SKph...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://secure-web.cisco.com/1R2xAoG-4D6Lo_1SB4QZ2cfxYjmIuCIrFEf64VhtY3cC05o...
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
freesurfer@nmr.mgh.harvard.edu
-
De Giorgi, Sara -
Fischl, Bruce R.,PHD -
Joshua K Lee -
Tang, Kaibo -
William Baare