External Email - Use Caution Many thanks for this. My experience so far with SAMSEG, SynthSeg---small sample so far. All images were obtained 3DT1 isomeric voxel. Just wanted to see how the two pipelines would compare.
2 subjects who went on 6 different clinical scanners, GE or Philips:listed below. The coefficient of variation in the structures I'm interested in was: normalized by the ICV (sbTIV, segmentation based TIV). *SAMSEG* interscan sbTIV NBrain-Stem Ncortical-vol NPutamen NCaudate NThalamus COV 1.620754 1.937988 0.996077 1.971807 1.863897 1.549882 *SynthSEG (normalized to ICV (sbTIV)--which was obtained from running SAMSEG on synthetic MRI (SynthSR):* Brainstem Cortical vol Putamen Caudate Thalamus 1.48696 1.61017 2.20072 2.51099 2.16196 Since head size does not change in the short period of time, my test subjects (n=50) repeated scan x 2 had a sbTIV coefficient of variation of 0.93 based on SAMSEG. Across the 6 clinical scanners that I used (listed below), I think there was enough tissue contrast similarities across the scanners to give a COV around 2%, which I think is NOT bad. Even in clinical trials with MRIs performed on the same vendor scanner across different sites, I think the goal is to produce variability < 2%. From what I can see from my data, I think you could compare across vendors with a reasonable overall COV of around 2%, that is if the biological effect is > 2% per time of interest. my best, AJ Scanners used for controls and test subjects: Achieva_TFE_R1 Achieva_TFE_R2 Ingenia_R1 Ingenia_R2 GE_SPGR_1529_R1 GE_SPGR_1529_R2 GE_SPGR_R1 GE_SPGR_R2 Phillip_Achieva_R1 Achieva_R2 GE_R1 GE_R2 On Sun, Nov 28, 2021, 20:41 Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Also samseg, see > https://secure-web.cisco.com/1vp8CpJRiQKmY2Jw2cEv7mIT6pEjTqFspCV00PtwvCROFBQ4enl56APRMm5vjCelLMOKTLsWx15btdt_HhgYgXyFx2liCxCnsyVuAie9mcFQKtBWyJCW52VClhUXJEaUpXlqzWLs5daHkP5TL9dUJ-iBFLSAzyXGsJH2wtHdkKGTDzh-wbeUSOVjMBNN73JLXj1DWaZd5PYDBBRcyuOXcE7q8qgXcZRkUXTWsCZ-QxenmUNJo0I-ZX_TRRmRXTl2iSj4S3VgFkY6HpZvnCw2QDxv6kepjoXi0vDAV9exqeEr_0pudttpPAtIHJVBeurZP/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F33940143%2F > > On 11/26/2021 11:16 AM, Fischl, Bruce wrote: > > Hi AJ > > you might try SynthSeg, as that is one of the advantages of it - it isn't > biased towards any particular MRI sequence > > cheers > Bruce > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AJ > <ajcns1...@gmail.com> <ajcns1...@gmail.com> > *Sent:* Thursday, November 25, 2021 9:00 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] SynthSR > > > External Email - Use Caution > Hi, > Could synthetic MRIs generated by the SynthSR script be potentially used > to harmonize T1w weighted images acquired on different scanners? Then used > harmonized images for volumetric analyses? > Many thanks > AJ > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/188j_UIaJs8RtWjL7jYdGjiSyaItct6743_nhSXU8bJ4xgJDNzAMr4iFMMSKeksjMFqpbdFPV-RzTlNRT06O8_5zwiCev10PughdsYCU7MAHXhK9QWbIcS7wVRyYmvVQ7qbX1pwyn1FJY85vDypLpqX_IE_v0GAA-W5t8r88u8SfWPlw5KfoOT3qEjQYrIPZUCA9MY8HE5hgs1Szkmx68oobGtcSOU-AfiJuzdKbEcwo3eBL0YLZ7fY3uMvOuY52W5ebbBBP3cl9HcITWySkm9LZOjJ_sVXd2Rxg8XcS8Ob_gHxnAnrrbMwTWjsiKrZZG/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 > http://secure-web.cisco.com/11i2c2KWvoLMVt2ut7uIJpV1Dz-5ld20D2TOclLSFMWwTPZpwDbbp4ramMU3POezM6R2i_0njPDSlVDbe706Mw5wBmQmtOSJFYTvjtJ4SwNJrG5uDz2QT17esffAtHGgvY7mg5DN5vfrHTyZ5mK_lkohUO8C5wI67qDwutDewam3UUhCbSObifg_xHOOorfKja9g2S1ZBM5QfuRkta2ZOoNBDtCEyk5wurc92r2YN1Zj5AxS_VAxtFiAH1iSR8M_oOucEcJ_3DnjwBr73KRJC6bP0P1inoJYDloWTy9bsEce6xU2H5Os5y4psoPbaA6G9/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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