External Email - Use Caution
Dear All,
we are running a project on brain morphometry in a clinical sample without brain injury. For most patients, we have both:
* T1W isotropic 1mm post-gadolinium * T2W TSE with 4mm axial slices
We would like to obtain high-resolution T1 images with SynthSR followed by standard voxel-based and surface-based processing in CAT12. I am wondering which contrast is best suited for our purpose, also considering that our clinical sample has no brain injury and the only blood vessels are enhanced in post-gadolinium sequences.
I made some attempts on both sequences for a couple participants and segmented them with CAT12. The overall image quality rating is almost identical. So is the estimate of total intracranial volume, with some differences in grey matter volume estimation (generally smaller in synthetized post-gado sequences vs synthetized T2) and CSF (generally bigger in synthetized post-gado). I haven't checked surface-based metrics.
I am quite new to the field, and I really appreciate your help!
Best, Lorenzo
Lorenzo Diana, PhD PostDoc
Advanced Imaging Research (AIR) Group
Swiss Paraplegic Research Guido A. Zäch Strasse 4 6207 Nottwil, Switzerland
Dear Lorenzo, Why not using the T1w images directly? Cheers, /Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: Diana Lorenzo lorenzo.diana@paraplegie.ch Date: Thursday, June 26, 2025 at 5:16 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SynthSR - T1 3D post-gadoinium vs. T2 FSE 4mm
External Email - Use Caution Dear All,
we are running a project on brain morphometry in a clinical sample without brain injury. For most patients, we have both:
* T1W isotropic 1mm post-gadolinium * T2W TSE with 4mm axial slices
We would like to obtain high-resolution T1 images with SynthSR followed by standard voxel-based and surface-based processing in CAT12. I am wondering which contrast is best suited for our purpose, also considering that our clinical sample has no brain injury and the only blood vessels are enhanced in post-gadolinium sequences.
I made some attempts on both sequences for a couple participants and segmented them with CAT12. The overall image quality rating is almost identical. So is the estimate of total intracranial volume, with some differences in grey matter volume estimation (generally smaller in synthetized post-gado sequences vs synthetized T2) and CSF (generally bigger in synthetized post-gado). I haven't checked surface-based metrics.
I am quite new to the field, and I really appreciate your help!
Best, Lorenzo
Lorenzo Diana, PhD PostDoc
Advanced Imaging Research (AIR) Group
Swiss Paraplegic Research Guido A. Zäch Strasse 4 6207 Nottwil, Switzerland
External Email - Use Caution
Dear Eugenio, thanks for your quick answer!
Just to be sure: by "T1w" you mean the post-gadolinium ones, right? Unfortunately, we do not have pre-gadolinium T1.
I was unsure whether the hyperintense vessels (especially, the venous system) could have caused issues when segmenting the GM/WM/CSF with CAT12. That's why we opted to use SynthSR.
My first choice would be to generate 3D T1 MP-RAGE from 3D T1 post-gadolinium because they are more similar in terms of resolution and contrast.
Thanks again!
Best, Lorenzo
From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, 26 June, 2025 3:29 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNE-EMAIL] [Freesurfer] Re: SynthSR - T1 3D post-gadoinium vs. T2 FSE 4mm
EXTERNE-EMAIL: Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge! Es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist.
Dear Lorenzo, Why not using the T1w images directly? Cheers, /Eugenio
-- Juan Eugenio Iglesias http://secure-web.cisco.com/16CbzjrPt9p6VlU19xrmdLWJ1C1-nHFsLLMqv1VYmmG5jDIs...
From: Diana Lorenzo <lorenzo.diana@paraplegie.chmailto:lorenzo.diana@paraplegie.ch> Date: Thursday, June 26, 2025 at 5:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] SynthSR - T1 3D post-gadoinium vs. T2 FSE 4mm
External Email - Use Caution Dear All,
we are running a project on brain morphometry in a clinical sample without brain injury. For most patients, we have both:
* T1W isotropic 1mm post-gadolinium * T2W TSE with 4mm axial slices
We would like to obtain high-resolution T1 images with SynthSR followed by standard voxel-based and surface-based processing in CAT12. I am wondering which contrast is best suited for our purpose, also considering that our clinical sample has no brain injury and the only blood vessels are enhanced in post-gadolinium sequences.
I made some attempts on both sequences for a couple participants and segmented them with CAT12. The overall image quality rating is almost identical. So is the estimate of total intracranial volume, with some differences in grey matter volume estimation (generally smaller in synthetized post-gado sequences vs synthetized T2) and CSF (generally bigger in synthetized post-gado). I haven't checked surface-based metrics.
I am quite new to the field, and I really appreciate your help!
Best, Lorenzo
Lorenzo Diana, PhD PostDoc
Advanced Imaging Research (AIR) Group
Swiss Paraplegic Research Guido A. Zäch Strasse 4 6207 Nottwil, Switzerland
Yes, I meant postGad. But yes, if contrast gives you trouble with CAT12, SynthSR (on the postGAD) seems like a sensible option. Cheers, /Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: Diana Lorenzo lorenzo.diana@paraplegie.ch Date: Friday, June 27, 2025 at 04:01 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: SynthSR - T1 3D post-gadoinium vs. T2 FSE 4mm
External Email - Use Caution Dear Eugenio, thanks for your quick answer!
Just to be sure: by "T1w" you mean the post-gadolinium ones, right? Unfortunately, we do not have pre-gadolinium T1.
I was unsure whether the hyperintense vessels (especially, the venous system) could have caused issues when segmenting the GM/WM/CSF with CAT12. That's why we opted to use SynthSR.
My first choice would be to generate 3D T1 MP-RAGE from 3D T1 post-gadolinium because they are more similar in terms of resolution and contrast.
Thanks again!
Best, Lorenzo
From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Thursday, 26 June, 2025 3:29 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNE-EMAIL] [Freesurfer] Re: SynthSR - T1 3D post-gadoinium vs. T2 FSE 4mm
EXTERNE-EMAIL: Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge! Es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist.
Dear Lorenzo, Why not using the T1w images directly? Cheers, /Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.comhttp://secure-web.cisco.com/16CbzjrPt9p6VlU19xrmdLWJ1C1-nHFsLLMqv1VYmmG5jDIsgMnOvtOG9I9dsXAlYl1vNtmGejsBbjPDYC0YMy3IfAyIqHvE0hpY7nkwaqxgDP0TloIbig2M0Lb_ipAi8qDpnRmIpm17fx3VDvZTmhh8L8h4LQZaPjp2kEQ5Jh2NXl-XB8MLFCUDXhc6u3IAwMLcx5qlSnC6ALPTKvBMWOuUW8kf6E5Ci2apnlmJhSSxI43Tv1pENsKiCfOg84i1nDju9higvsC3nPLyll1PkrF35fBZVFGVYnkaM9ShfMHjXeW6NVACt0QmaSEX0vmBV/http%3A%2F%2Fwww.jeiglesias.com
From: Diana Lorenzo <lorenzo.diana@paraplegie.chmailto:lorenzo.diana@paraplegie.ch> Date: Thursday, June 26, 2025 at 5:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] SynthSR - T1 3D post-gadoinium vs. T2 FSE 4mm
External Email - Use Caution Dear All,
we are running a project on brain morphometry in a clinical sample without brain injury. For most patients, we have both:
* T1W isotropic 1mm post-gadolinium * T2W TSE with 4mm axial slices
We would like to obtain high-resolution T1 images with SynthSR followed by standard voxel-based and surface-based processing in CAT12. I am wondering which contrast is best suited for our purpose, also considering that our clinical sample has no brain injury and the only blood vessels are enhanced in post-gadolinium sequences.
I made some attempts on both sequences for a couple participants and segmented them with CAT12. The overall image quality rating is almost identical. So is the estimate of total intracranial volume, with some differences in grey matter volume estimation (generally smaller in synthetized post-gado sequences vs synthetized T2) and CSF (generally bigger in synthetized post-gado). I haven't checked surface-based metrics.
I am quite new to the field, and I really appreciate your help!
Best, Lorenzo
Lorenzo Diana, PhD PostDoc
Advanced Imaging Research (AIR) Group
Swiss Paraplegic Research Guido A. Zäch Strasse 4 6207 Nottwil, Switzerland
freesurfer@nmr.mgh.harvard.edu
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Diana Lorenzo -
Iglesias Gonzalez, Juan E.