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Hi Jessica,
I thought I answered this question already a couple of weeks ago -- Samseg ( https://secure-web.cisco.com/1mAdYI33jXHEKetoWeDXq9SIl5yaoShspvHPYQTfknokhVE...) 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:
External Email - Use CautionHello,
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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