You might be able to run both through longitudinal samseg as samseg will create a "base" image from both and try to bias correct both with respect to this image.
On 7/21/2021 1:31 PM, Fischl, Bruce wrote:
There isn’t really anything available for the latter approach. I would suggest the former and potentially including site as a nuisance variable. You very much want to balance across site in terms of whatever effect you are looking for (e.g. don’t scan all your patients on one and all your controls on the other)
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *AJ *Sent:* Wednesday, July 21, 2021 1:15 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Intensity equalization
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Thank you so much for your reply.
I have subjects who got MRIs on either GE or PH. There are mild image intensity differences between the two scanners. To combine volumetric data from both scanners, an easier way would be to express volumes as percentage of sbTIV (a less variable measure than eTIV) from respective scanners using SAMSEG. Or more involved process would be intensity normalization of scans to each other and then subsequent SAMSEG analysis. I think the former approach is easier and still valid? The later approach would require an additional program, if you would suggest one?
Many thanks
AJ
On Wed, Jul 21, 2021, 09:40 Fischl, Bruce <BFISCHL@mgh.harvard.edu mailto:BFISCHL@mgh.harvard.edu> wrote:
Hi AJ No, not easily. Maybe you can tell us your overall goal to see if we can help? Cheers Bruce *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> *On Behalf Of *AJ *Sent:* Wednesday, July 21, 2021 1:27 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> *Subject:* [Freesurfer] Intensity equalization * External Email - Use Caution * Hi, I have 2 MRIs on different scanners. The tissue contrasts are slightly off and there is slight differences in the volumes of ROIs. Is there a way to make both MRIs have the same intensity? I.e., Im2's intensity follows Im1's intensity? Many thanks AJ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1MddmNxzpm7K_dUp9KAdh-1y7LMeorgLFMIczH4RUjrPkHFi5GYXEIN5oOvrd9DWwq58ovjEgn3amynpRCVb-XsblTkzZLhVFDs34MrvbFk8flj9FKM-XKlFqw4tDF9oEIG7gSf2cruWMBKKg3DZbVxL99CRqoHuDQTLUf7dI69chmio_ivph5aQu-KtpVmM1Tvh0e0sV9AnrYMdcJjqBgc2CEtH2LgiSBumdV1OAIhQzc_axqQjLxGzd8Bd2sFJG98cgQ_4u-ob0kh-cy6K57A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1CGTcPlzVh7azBeQXbhtBR-yp3JBMGe_NQtLxcgxPmw--DXowonWvUKI57FKlZef6-rAJseGDzNIMpQg58xrdVm-m-m76gb7WvJ6pIX6_whCEYefkBHGgc7-QACgz_mGcg4m4ag4ljFcXNxKbpBs0kpvQT93XcdDrPpmu-etQ63LvEmy3B9SVIYZJej5pi-mucbzOR8QiOdpjG8kO9hWUx0pHm_78keP5YdDwa7_xT5ye00t_80EZf3Oj7m05eqcjBDNVFJ7PKYahrpoc9PuTIg/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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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