External Email - Use Caution
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
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
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: 56-9-97771785MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://scholar.google.com/citations?user=LO7LZ3oAAAAJ
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.researchgate.net/profile/Gonzalo_Rojas2MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://cvn.fecyt.es/0000-0002-6228-2678
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.researcherid.com/rid/B-2036-2013
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://cl.linkedin.com/in/gonzalorojascostaThe 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/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.
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/complianceline .