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Hi Bruce,

Thanks so much for the quick reply.

We have images from two studies that have two different T1 acquisitions. Both have 1 mm3 voxels but have different TR's (2300 vs. 2500 ms), TE's (2.26 vs. 2.9 ms), TI's (900 vs 1070 ms), etc. They were all acquired using the exact same Siemens Prisma scanner. We unfortunately cannot prospectively harmonize the T1 acquisitions as 50+ subjects have already been run through both studies. Both studies are focused on adults ages 18+ with moderate-to-severe cannabis use disorder, and are decently matched demographically (study 1 has an average age of 31, 64% male, while study 2 has an average age of 30, 70% male).

Are there any fatal flaw reasons why we cannot combine their FreeSurfer outputs?

Thanks!

Kayti Keith Research Specialist I Medical University of South Carolina Department of Neuroscience Center for Biomedical Imaging 68 President Street, BE220 Charleston, SC 29425

On 7/2/19, 12:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

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Hi Kayti

that's pretty hard to say. Even a few ms of TE for example can make a pretty big differeence in e.g. avoiding dura. In general of course we try to fix the acquisition parameters and at the very least balance your populations across different scan types. Can you give us more details or an example? Bruce

On Tue, 2 Jul 2019, Keith, Kathryn wrote:

> > External Email - Use Caution > > Hello, > > > > I’m curious if anyone has any insights about comparing T1s from different subjects that have > different acquisition parameters in Freesurfer. I’m trying to get a feel for how different is too > different in regards to comparing differently acquired T1s with Freesurfer. Are there any parameters > that must stay consistent in order for Freesurfer to generate comparable outputs between subjects? > Any other thoughts? > > > > Thank you! > > > > Kayti Keith > > Research Specialist I > > Medical University of South Carolina > > Department of Neuroscience > > Center for Biomedical Imaging > > 68 President Street, BE220 > > Charleston, SC 29425 > > > > >

Hi Kayti

it's hard to say a priori. Run them all through and see how bad the scanner effect is. Depending on which scans have which parameters some of your differences may cancel or they may add.

cheers Bruce

On Wed, 3 Jul 2019, Keith, Kathryn wrote:

   External Email - Use Caution

Hi Bruce,

Thanks so much for the quick reply.

We have images from two studies that have two different T1 acquisitions. Both have 1 mm3 voxels but have different TR's (2300 vs. 2500 ms), TE's (2.26 vs. 2.9 ms), TI's (900 vs 1070 ms), etc. They were all acquired using the exact same Siemens Prisma scanner. We unfortunately cannot prospectively harmonize the T1 acquisitions as 50+ subjects have already been run through both studies. Both studies are focused on adults ages 18+ with moderate-to-severe cannabis use disorder, and are decently matched demographically (study 1 has an average age of 31, 64% male, while study 2 has an average age of 30, 70% male).

Are there any fatal flaw reasons why we cannot combine their FreeSurfer outputs?

Thanks!

Kayti Keith Research Specialist I Medical University of South Carolina Department of Neuroscience Center for Biomedical Imaging 68 President Street, BE220 Charleston, SC 29425

On 7/2/19, 12:07 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

CAUTION: External

Hi Kayti

that's pretty hard to say. Even a few ms of TE for example can make a pretty big differeence in e.g. avoiding dura. In general of course we try to fix the acquisition parameters and at the very least balance your populations across different scan types. Can you give us more details or an example? Bruce

On Tue, 2 Jul 2019, Keith, Kathryn wrote:

...

    External Email - Use Caution

Hello,

I’m curious if anyone has any insights about comparing T1s from different subjects that have different acquisition parameters in Freesurfer. I’m trying to get a feel for how different is too different in regards to comparing differently acquired T1s with Freesurfer. Are there any parameters that must stay consistent in order for Freesurfer to generate comparable outputs between subjects? Any other thoughts?

Thank you!

Kayti Keith

Research Specialist I

Medical University of South Carolina

Department of Neuroscience

Center for Biomedical Imaging

68 President Street, BE220

Charleston, SC 29425

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