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Kasperek, Jessica

15 Jul 2026 15 Jul '26

2:57 p.m.

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.

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Koen Van Leemput

18 Jul 18 Jul

4:09 a.m.

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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 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.

Andreas Bartsch

19 Jul 19 Jul

8:35 a.m.

New subject: Samseg

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
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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.

Koen Van Leemput

5 Aug 5 Aug

6:24 a.m.

New subject: Samseg

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 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/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 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 to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e... https://secure-web.cisco.com/1R0IJdM01-suN-1sGoK6w0hdonQMlX5_SIjuhYejxGUAfK4NiNR3QbKtabsOiONLgUuTNiWiCSgOTiyc9xqGwhgabCMf27jRyCJ-eYv6lEI0gZ2zQNe8U83IkYDaUNYGDSijnKZbD8x1frn69V_pF8zF-vYlR8pBK_93xAGHAMxCYFobfaSGVyftKZalQY96yPw-zBX3yDQG6GEI2sdRIH9m8h0QnNbVvbfjEql8fGCKlF5hbz4NlhnqaRImKHmAomXqHq7IvAXYFzYka3-ifVEg5Th4_qm_P3j__3vJSy0aYp_oT1JITeyGKidQDU9S3lfPmYurgx0vdDu88RI99fQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F 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 at https://secure-web.cisco.com/1XRhFxw0-v2Rw30LVkSislL68yZ6CVSq0NCbv1gu-GTdjEo... https://secure-web.cisco.com/1JZssYZdLPbj-uAktp2oDyzHhXy6ZunM89Cw3q_okutZwJ2LSNOcaoMDyZdLwgG7s3zcagm_CixSgl4GpigHNXfVXdeopzhe6nwLntEMTtbmzuwJpjI7HJ3hi-D1d8Ih76DbD9dINs6RM0mgmed-DlrVZH23WVMBHUxacIPI4IgyuwD23ZLlUumv5PKbdR5ZZ18wH5rRbcmsFtyM3k1oU3XT6TZWRj8E7kxH62WEjwoo4yHOba9Pq2YolEzhFXkERtl9k97XjckR47ofeqozSvRJ6OUUD-VnG9JDgY7-33IZRT6L9f-3GlOjdhJqWeDQIX7lTHFuf7CpxlULYdhTxzg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline https://secure-web.cisco.com/1XRhFxw0-v2Rw30LVkSislL68yZ6CVSq0NCbv1gu-GTdjEodINBV4N3rJfQ23NcEAIhwWzs6D6wEI_2gQ-EXBy2xNhAhW7nXtiRHX93Y1t6A1TRgK6s0AtyDwIL4EAfkQsdcnn3hHH7ivYdpvU0mkjzYX3G9engF9mu4c5F0KStnCfKk94RReDQiH57Pf2dkglWSqPWAfaFxV6rRdMzfXmm34FePnofeYPUvH1Kf-jYE3gPHfF2HMS6d7aDjmeLmLIu9ls1OhPmxjqeDjyRE8wH4sZ5DCdyFByHSTsDuGX6VKkTSQCK4Hv-ZjOaT3fRLOVKMiSRvsqdHtLopBgqhb2w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline 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.

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https://secure-web.cisco.com/1SS48nx_s9nhOnqaBcs4-wN_JYFu7yoBgiz0sHfflZpdM8e... 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 at https://secure-web.cisco.com/1XRhFxw0-v2Rw30LVkSislL68yZ6CVSq0NCbv1gu-GTdjEo... < https://secure-web.cisco.com/1XRhFxw0-v2Rw30LVkSislL68yZ6CVSq0NCbv1gu-GTdjEo... .

Andreas Bartsch

2:47 p.m.

New subject: Samseg

External Email - Use Caution

Thanks, Koen!

Yes, that makes sense.

And yes, much-much harder than one might think - for both instances you've mentioned.

Cheers,

Andreas

Am 05.08.26 um 12:24 schrieb Koen Van Leemput:

...

External Email - Use Caution

Hi Andreas,

Apologies for the delay in replying.

Hope this helps,

Koen

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

        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/1cnrdZymRk0HCqg3HIT4D4fs_R0sJ1CyEdZDdbkgw4U29AIw5qSEABp-1hkxuNRq9u2U8iHE-aXHIX3_u_njy1Q_RHhWm2DeN1oRr4MXPCIivhhkf4bTVNSqOj7tMmtTgJZbSJzOF4XANoF8bzRrooMB4gBpZZRDDKd5ZOycfLPzGWeL5O-OZFm7Sd-YBstIsDvmXr8dnaSCvOMvPNJhP1fVZYj0JcYK9eVmI-WTzPXQfyQTMpela9YMQLY5GBzmlSh29ZKx8n4pJjDjOUaqLxvXaWq1cpE4PR77Be3x82NM5_7ZlUxvPH6NHNK-Al19WsrbN3ILEUvYrkXjNayZX7A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg
<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.


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Andreas Bartsch
Kasperek, Jessica
Koen Van Leemput