On Sun, Jul 19, 2026 at 2:36 PM Andreas Bartsch <bartsch@radvisory.net> wrote:

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Hi Koen,

great to learn about Samseg.

I especially find the longitudinal stream interesting for MS lesions.

Can new or enlarging lesions be detected using the output classification? I.e., by simple subtraction if these are in the same image space.

Can you elaborate a bit? Was your main objective lesion segmentation or brain volume?

Cheers,

Andreas

Am 18.07.26 um 10:09 schrieb Koen Van Leemput:
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Hi Jessica,

I thought I answered this question already a couple of weeks ago -- Samseg (https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg) should be able to do most of what you need. There are a few things it won't do, though: spine lesions, new lesions, and prefrontal cortex.

Hope this helps,

Koen

On Wednesday, July 15, 2026, Kasperek, Jessica <jessica.kasperek@endeavorhealth.org> wrote:

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Hello,

One of my research studies, a retrospective Multiple Sclerosis (MS) study, is looking to conduct analyses on volumetric changes in brain MRI scans of MS patients during the course of their treatment. Specifically, it is looking for these items:

Overall brain volume change

Total lesion load

Cervical spine lesion

New MRI lesions

Asymmetrical atrophy between left and right hemispheres

Hippocampus

Thalamus

Basal ganglia

Prefrontal cortex

Cerebellum

Cortical GM

Each patient has approx. 10 MRI scans or so. Is this a doable project for FreeSurfer? Any recommendations on how to approach this with the software? Any help is appreciated as there is no one at my institution that could direct me with the appropriate steps.

Thanks,

Jessica

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