External Email - Use Caution        

Hi Lilla,

Thank you for the quick response. We have a dataset of preterm born neonates who are all scanned at 40 weeks PMA, so from a developmental point of view, they are all 'neonates' of 0 months. We would now like to find the PLIC (posterior limb of the internal capsula) of every neonate, but drawing these manually would take a lot of time. I was wondering if infant_recon_all or freesurfer can be used to find such a ROI in all subjects. Basically I would like to add/replace another label in the template, but there is no single template in the infant pipeline of course.

If you would need any more info, please let me know.

kind regards,
Maarten
 
From: Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edu>
Sent: 09 April 2026 18:37
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Maarten Naeyaert <Maarten.Naeyaert@uzbrussel.be>
Subject: Re: custom ROI in infant_recon_all
 

Opgelet! Dit emailbericht is afkomstig van buiten UZ Brussel. Open geen bijlagen en klik niet op links indien u twijfelt over de afzender of de inhoud.

Hi Maarten,

Thanks for your question. Please, reach out to me directly with the details as my answer might depend on those.

Lilla
From: Maarten Naeyaert <Maarten.Naeyaert@uzbrussel.be>
Sent: Thursday, April 9, 2026 10:17 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] custom ROI in infant_recon_all
 

        External Email - Use Caution        

Hi freesurfer developers,

We're infant_recon_all (in freesurfer 8.1.0) on a dataset consisting of newborns, but would like to include a custom ROI not yet included in the infant atlas. Is there way to do this?

Best regards,
Maarten Naeyaert

--------------------------------------------------------
Maarten Naeyaert, PhD
MR physicist

Department of Radiology UZ-Brussel
Vrije Universiteit Brussel (VUB)
Laarbeeklaan 101
1090 Brussels
Belgium
Tel: +32 (2) 477 53 88
Maarten.Naeyaert@uzbrussel.be

Bureau: MRI 1-2 (routenummer: 950)

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://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.