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://www.jeiglesias.com

 

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

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.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

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