External Email - Use Caution
Hi Andreas,
Apologies for the delay in replying.
We did not consider quantifying new or enlarging lesions specifically, although I guess you could get that information as a postprocessing step along the lines you suggested. Rather, our aim was not only to robustly segment lesions, but also to quantify normal brain structures (harder than you might think when lesions are present) and to make sure no false lesion detections pop up everywhere when a healthy control is the input (also harder than you might think...)
Hope this helps,
Koen
On Sun, Jul 19, 2026 at 2:36 PM Andreas Bartsch bartsch@radvisory.net wrote:
External Email - Use CautionHi 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:
External Email - Use CautionHi Jessica,
I thought I answered this question already a couple of weeks ago -- Samseg (https://secure-web.cisco.com/15Cf8qhJY0GU0WBxUbx21BAV01Sjna1DzA_ceAQlMV5bk8s... https://secure-web.cisco.com/1mAdYI33jXHEKetoWeDXq9SIl5yaoShspvHPYQTfknokhVEAunCrwYb2YQlyeoqacj5MUueGjnD-bnAfPlsgA20dnBNMJOz4egsUvGu8PY96QSzDpMGvehSjilfEQvuLN5Y1v78AjAJZb97_VAZFWcxnhOZ60ZVdgKB8k2rPAqfqmkauE8PI-B73St-nwDPVE5kKpk3E0L1cRfvfOe1tQ65EqZm6KUTlZCplajiPkVoYI0rskY_GLg7hgLUbVVMdKQb6OZCKomOUHFXzuwhqe8cYq24clv008r3G4Hdk4sz1EXkHZw-bqcK5B5oF2MHceqsBWrfLoyuXeATSRwxU9VA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg) 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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