Hi Inga, Could you share some screenshots and the age-at-scan of your subjects? Thanks, Lilla ________________________________ From: Harting, Inga Inga.Harting@med.uni-heidelberg.de Sent: Wednesday, March 8, 2023 10:18 AM To: Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: AW: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation

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Hi Lilla,

I got infant_recon_all to run through, but the segmentation did not produce the subcortical results I was hoping for. Looking stepwise at results it seemed as if the registration process “bloated” the central structures = basal ganglia, internal capsules (email and your answer below).

I’d be happy if you have any suggestions looking at the label fusion step.

Best regards, Inga

Von: Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu> Gesendet: Montag, 6. März 2023 17:18 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: Harting, Inga <Inga.Harting@med.uni-heidelberg.demailto:Inga.Harting@med.uni-heidelberg.de> Betreff: Re: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation

Hi Inga,

Sorry, I missed this message on the mailing list.

This is a new issue to me, so I will take a look at the label fusion step.

And yes, we are working on including T2w images in the pipeline as at the newborn stage it would help with the GM/WM segmentation accuracy.

Best, Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Inga Harting <inga.harting@gmx.demailto:inga.harting@gmx.de> Sent: Monday, October 31, 2022 3:11 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Inga_klinik <inga.harting@med.uni-heidelberg.demailto:inga.harting@med.uni-heidelberg.de> Subject: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation

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Hello experts,

I've begun using infantFS for neonates and I'am interested in the subcortical segmentation.

I noticed that the internal capsule is delineated in the manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's having gmwm or not), but that ist lost after mri_label_fusion when the thalamus has suddenly increased, swallowing PLIC and corona radiata, the basal ganglia have also expanded and the corpus of the caudate nucleus is large and pushed upwards.

Is there a way to preserve the subcortical anatomy?

Would labelling e.g. capsula interna help? Is there a way to include 2D T2axial to help with gmwm contrast?

Best regards, Inga.

-- Dr.med. Inga Harting

Dpt. Neuroradiology Heidelberg University Medical Center INF 400 69120 Heidelberg inga.harting@med.uni-heidelberg.demailto:inga.harting@med.uni-heidelberg.de

Mühltalstr. 124b 69121 Heidelberg inga.harting@gmx.demailto:inga.harting@gmx.de

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