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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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AJ ajcns1969@gmail.com Sent: Thursday, November 25, 2021 9:00 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SynthSR
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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
Also samseg, see https://pubmed.ncbi.nlm.nih.gov/33940143/
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AJ ajcns1969@gmail.com *Sent:* Thursday, November 25, 2021 9:00 PM *To:* Freesurfer support list 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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@mgh.harvard.edu wrote:
Also samseg, see https://secure-web.cisco.com/1vp8CpJRiQKmY2Jw2cEv7mIT6pEjTqFspCV00PtwvCROFBQ...
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AJ ajcns1969@gmail.com ajcns1969@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 CautionHi, 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 listFreesurfer@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_nhSXU8bJ4xgJ... 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-5ld20D2TOclLSFMWwTPZp... . 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.
Are you correcting for gradient distortion? That could easily make 2%. It looks like you used different ROIs in your comparisons.
On 11/28/2021 10:14 PM, AJ wrote:
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 dgreve@mgh.harvard.edu wrote:
Also samseg, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://pubmed.ncbi.nlm.nih.gov/33940143/ <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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AJ <ajcns1969@gmail.com> <mailto:ajcns1969@gmail.com> *Sent:* Thursday, November 25, 2021 9:00 PM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto: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 list 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/188j_UIaJs8RtWjL7jYdGjiSyaItct6743_nhSXU8bJ4xgJDNzAMr4iFMMSKeksjMFqpbdFPV-RzTlNRT06O8_5zwiCev10PughdsYCU7MAHXhK9QWbIcS7wVRyYmvVQ7qbX1pwyn1FJY85vDypLpqX_IE_v0GAA-W5t8r88u8SfWPlw5KfoOT3qEjQYrIPZUCA9MY8HE5hgs1Szkmx68oobGtcSOU-AfiJuzdKbEcwo3eBL0YLZ7fY3uMvOuY52W5ebbBBP3cl9HcITWySkm9LZOjJ_sVXd2Rxg8XcS8Ob_gHxnAnrrbMwTWjsiKrZZG/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list 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/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 *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/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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These are the same ROIs, just labeled differently by me late at night. They are all normalized by the ICV. Just didn't add the N next to the ROI in a different row.
Good point. I am not correcting for gradient distortions. Will do.
Many thanks AJ
On Sun, Nov 28, 2021, 21:40 Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Are you correcting for gradient distortion? That could easily make 2%. It looks like you used different ROIs in your comparisons.
On 11/28/2021 10:14 PM, AJ wrote:
External Email - Use CautionMany 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 dgreve@mgh.harvard.edu wrote:
Also samseg, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1cS13xAGgITfUHMGUyFsvweyVHbmcsaFQ23MTyl96k0V_BX... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AJ ajcns1969@gmail.com ajcns1969@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 CautionHi, 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 listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1QhFmTXCfi2HiS1aDKz0TMt25WAH7a67WZbOPeg-vsSYv3J... 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
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Fischl, Bruce