External Email - Use Caution
Ok... Thanks you very much...
Gonzalo Rojas Costa
On Wed, Mar 8, 2023 at 5:38 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
I added a flag (--ct) to mri_synthsr in FreeSurfer so people don’t need to clip manually when they process CT scans. It should be on the publich development distribution in a couple of days 😉
Cheers,
/E
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1IR1bx4iIiu483c-gubT-7sJz9-PHRZ1A5blSSl0RB6i-5Oq...
*From: *Gonzalo Rojas Costa gonzalo.rojas.costa@gmail.com *Date: *Wednesday, March 8, 2023 at 13:56 *To: *Benjamin Billot bbillot@mit.edu *Cc: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu, " freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: SynthSeg with CT images.
External Email - Use Caution *Hi Benjamin:
I tested with the clipping, and it works ok with a CT image.
Sincerely
Gonzalo Rojas Costa
El mié, 8 de mar de 2023, 14:39, Benjamin Billot bbillot@mit.edu escribió:
Yes, agreed.
Gonzalo: Also, if SynthSeg still gives you a bad result after clipping, you might want to check that the image header is not corrupted.
Best
Benjamin
*From:* Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu *Sent:* 08 March 2023 12:25 *To:* Gonzalo Rojas Costa; freesurfer@nmr.mgh.harvard.edu *Cc:* Benjamin Billot *Subject:* Re: SynthSeg with CT images.
Dear Gonzalo,
Can you please try clipping the input to Hounsfield between 0 and 80? That should do the trick. If you have trouble with this, feel free to send me scan so I can take a look.
Benjamin: maybe we should add this as a flag, as we do in SynthSR…
Cheers,
/E
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1IR1bx4iIiu483c-gubT-7sJz9-PHRZ1A5blSSl0RB6i-5Oq... http://secure-web.cisco.com/1rajmSb1Z4X6hrVV7EC5tsUxk0uanEzSaSYaYxD1Egdh8AR6Hh56R4ftwHZ3VwShD-6P853CFDNvr-rulTBK7nI6zB590521zSlI2xndRFDCTdFQXWFZL71cI_nMoxCgFP2x-BPYJbfesBsX4B1BhoDD2zLwAc83S9NaHWxY8RXJEaAQooyHB7jyvHnWH5fSABbS_u5Nqs3Qji4RAvUerQ_3i9ndWjZDbjgWJtZrfaq3pdmNg-8NkfZsxg2-FXvLwnlOlA0BmnXCLqIPGpVLSD_9yxZ5510Lh7AGotI4m7DiXg2r_VRVsm9GY0qA9CTDIW7yIxkTUu8a-4i7mNB2UEA/http%3A%2F%2Fwww.jeiglesias.com
*From: *Gonzalo Rojas Costa gonzalo.rojas.costa@gmail.com *Date: *Wednesday, March 8, 2023 at 12:04 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Cc: *"Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu *Subject: *SynthSeg with CT images.
External Email - Use Caution *Hi:
I tried SynthSeg using CT images, but I got very bad results... CT images must have some specific characteristics? I tried with axial acquisition and volumetric one....
Sincerely,
Gonzalo Rojas Costa
Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785
https://secure-web.cisco.com/1KzPea1YxgjqNRqHWvcKvdH1ho2b0l5JLB0r09f8HMdtZFB... https://secure-web.cisco.com/1X4JTWBblTD8tld8oBtoX_hRATMKAHXt1kz8xQ7YPlXYPCFqdXfA0H2JSQd7Sf9iABw7ZXWREb6ZPRpqIjLu5kUVANuSPsw4E1FQrq8EcNcxVJLcJP8_61lsQFWfJtoEXAXr8kACcKq_PDEnngdLDzo-x-Napt2ob06RC1xuPwm1RwJWaPMun-E7X8rrcjsD6xf4UupYvJDfj8OSi7Cvnpey6_7zNIF4GBjHNUOcHEG-Ie9_RuFiTgQfOuTTQi1XDQmJ06W2r5MDwitXqElbSh7QTBTa6CxuYVhc03x81FuP1eS1BiUMk4yxWVGvd2JnzDm38adwdkUrQ4Esm7Ojhsw/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oAAAAJ https://secure-web.cisco.com/15WUSvOlDCd8gZLVKogIZYlhmV9KT_lzIEGdy9rBrhDdMke... https://secure-web.cisco.com/1jIR1VD1EGr6FdxqTGgScWCn_mHW5DPrMZAjfRggLiGtOamcGRinZiM0HNnQE0ybVKUqF9WJYOq9a4QJzt0qFHoBw_eIv85hrkDL1pJNd7WrTFbj1RjcPFatMfv-bsxG8I7zoXYh2maIFCWC4iz5ELXiKCr1WTkvsIeZXu5mQCEkJ3eB4sCbN5x-CT5YEOaxPEJdOQ_t3mNDKTN5ORe8om-TzD7U8VDs-P68_-68BvQm3f7CDK_xEW4nPWvaGT7Icx1cqkRXMZKWzs340o4vkCM4EJJ-o0J_RuNGaGs91o5BtOKE6AE0cFdL_6s2NTOKhD2uLQp3ofHyAuuQKkr72vw/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2
https://secure-web.cisco.com/1itktqCbpkNPFYGcAjerJU_K8UAvCKHA3SOSXJs6guQ2X8s... https://secure-web.cisco.com/1yA9l7ISJLI6AsyMtjg6tqVLF4b_n1UlUVhia2mXbDUAX5fGZyZcRqNTfuohp8mAbc_ACa3hgSPYntMqG1-0fDtSgts2OmLxz4QnX6ZHQZKM5PyA7BrbGBzONTFUBMDYgc9zYNZbdJe4xL_hLWAo2R4UEFgI5rD87fHAWQabgaZwrGmQo79CFJvlemPIiBO2e7KxArWWjicG-y_ekICfjdeLuFvdQ-w0tXfXupw3t0jYHJ_XemfYZZSYZnP0Q_2UclHE7ZpsQ_uAGCpXBiR2TmPLXbCn5PG0hA4Drp3aBhP-kW9P-NRZeMBjGO6M-grFIu4fwZrTuuKF6wHpDWR0qWQ/https%3A%2F%2Fcvn.fecyt.es%2F0000-0002-6228-2678 http://secure-web.cisco.com/1WC9LAqwZ4KVsjNwjXXUe8iFeQzf6tv57qOj_mjPPp_6vxyu... http://secure-web.cisco.com/1WbHoWnrfeHvPRvJjfNf_577rSGYT1ApJAnQKa2Hbt1JxqbBvW3yNeTFIJZhl6BJGKU5bn0BFseKD5SbdgzeGZXl9W5z_RLkxMO3tMJ3Ho7EimcZsInft7fSljrQ8unGnsbL3GURvWX9kt3iutb_FKFOwbHjFq6Vfk98f5ln4uKfUHTK8Sz_oHjvvyccS3R3Pg5QKPmh8wxwGN2DOUx2oP5LesBqeYLf2qZuOcuxOFUxIlCHsGkvY7sCIQVkae_uCtlklxMOBWMAsQdHFjG7j_3U1BZSigYA8URPVjYLmvq9rmRDxFkOMvweirFk1J0VYnmuRf_N4KM3kEE53S6FIyw/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013 https://secure-web.cisco.com/1pA083y_iLDvuu4h5uYEILl0PodD26ncwuUVl8EHIoXQAKW... https://secure-web.cisco.com/1ZasoGFuD7Kwh5m95aUJSJ7Cq9E3amXs01l9LmTC_TxXWGvNXoUNsQhbXAsKeEpwqtY4DKxxagBBuD4DytiQwUREeKPADZfRMh1UMYBkVeHwzmYFMbeRy0n0FENBHCrqjuaMPIlvbxQgCBFBxBbUnbwrsjIxqvYuiS4j9vOXm7HyCS3BZmODfmvJZeq5sJpS8X3LgF6gCz_P4GUPTwQN0rmQMsUyDehQmYabjMbBg14zRFwrKdbKawRFOXFF4rsNzs52H1LIgz4SV12ffYLdV-e-br5KKz4A0FdWreZrz7pQdiyS_pRNhW6z2qwgc89ux1hi9UW6zoP9RmoozejIZEw/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta
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/1k3vKHEMBlV8u303HFBqgkuXRjM257Fw71Kg6ktuLKoy1Vs... https://secure-web.cisco.com/1vxTLaPNIqDK-95PFDEbjy7JEt0lztex5hj4Og6535g9iVzHquwLg6ypKfz8nXeBzwq7NzxGPymsgw6L02Qzn9EZds4psY95HFke-E4PpftliM70oUJBBLdSo87rkzuUeOc84xswU3t-qgLoglsb4e7QRvFbmcwuqOcpVrMTsaMdvszoXDwxlZ41_UgI3q9k3wNqa6i-4pHMlpOkAHElFl-NqpyIFUIx0NCvAfZnnyG8ytvhddPTrUBtyzT3AqMrHE2MlLbsULixUtjnRVM_TaUvPEOVqjB0eBgXto9RdCi-9Jk94w1dBvqLmH3heF6SdYms5bwiDLiGCY1sDxb6zWA/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.
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/1k3vKHEMBlV8u303HFBqgkuXRjM257Fw71Kg6ktuLKoy1Vs... .