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:

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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/

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

 

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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

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