External Email - Use Caution
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:
External Email - Use Caution
Hi Jessica,
I thought I answered this question already a couple of weeks ago -- Samseg (https://secure-web.cisco.com/1CE52lFSIYS9gAFjS2dWkuPQCP7oICcYN3QqwSL-7wSQi91... 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 Caution 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 ******************* PLEASE NOTE ******************* This message and any documents accompanying this transmission may contain information that is privileged, confidential, and/or exempt from disclosure under applicable law and is intended solely for the addressee(s) named above. If you are not the intended addressee/recipient, you are hereby notified that any use of, disclosure, copying, distribution, or reliance on the contents of this message is strictly prohibited and may result in legal action against you. Please reply to the sender advising of the error in transmission and immediately delete/destroy the message and any accompanying documents. Thank you.
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1R0IJdM01-suN-1sGoK6w0hdonQMlX5_SIjuhYejxGUAfK4... 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 athttps://http://secure-web.cisco.com/1DGeG4aNz65FTtPV_oeDN-_JJg9TrWJwJWIgvhUT... https://secure-web.cisco.com/1JZssYZdLPbj-uAktp2oDyzHhXy6ZunM89Cw3q_okutZwJ2LSNOcaoMDyZdLwgG7s3zcagm_CixSgl4GpigHNXfVXdeopzhe6nwLntEMTtbmzuwJpjI7HJ3hi-D1d8Ih76DbD9dINs6RM0mgmed-DlrVZH23WVMBHUxacIPI4IgyuwD23ZLlUumv5PKbdR5ZZ18wH5rRbcmsFtyM3k1oU3XT6TZWRj8E7kxH62WEjwoo4yHOba9Pq2YolEzhFXkERtl9k97XjckR47ofeqozSvRJ6OUUD-VnG9JDgY7-33IZRT6L9f-3GlOjdhJqWeDQIX7lTHFuf7CpxlULYdhTxzg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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.