External Email - Use Caution

It is the file computed longitudinal processing that represents the rate with respect to the thickness at the first time point computed by long_mris_slopes.

Swati

____________________________________________ Swati Rane Levendovszky, PhD Interim Director, Diagnostic Imaging Sciences Center Assistant Professor, Integrated Brain Imaging Center Radiology University of Washington Box 357115 | AA035 HSB | Seattle, WA 98195 srleven@uw.edumailto:srleven@uw.edu | Ph: 206 543 6159 Web: https://sites.google.com/site/uwswatirane/ ____________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, January 16, 2020 at 3:26 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

Sorry, what is "pc1"? On 1/14/2020 9:44 AM, Swati Rane wrote:

External Email - Use Caution Hello,

I was wondering if someone could answer my question below

Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files.

Are there any set of parameters that should be set differently when using pc1 instead of thickness files?

Thanks! Swati

____________________________________________ Swati Rane Levendovszky, PhD Interim Director,Diagnostic Imaging Sciences Center Assistant Professor,Integrated Brain Imaging Center Radiology University of Washington Box 357115 | AA035 HSB | Seattle, WA 98195 srleven@uw.edumailto:srleven@uw.edu | Ph: 206 543 6159 Web: https://sites.google.com/site/uwswatirane/ ____________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Swati Rane srleven@uw.edumailto:srleven@uw.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, January 10, 2020 at 10:06 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

External Email - Use Caution Hello FreeSurfer Developers,

I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you could use the multiple comparisons corrections that come with it but does not comment on using the mri_glmfit-sim option.

I just want to confirm whether there is anything prohibiting me from using mri_glmfit-sim. Are there any set of parameters that should be set differently when using pc-1 instead of thickness files?

Also, would you do a stricter correction and stick to the longitudinal model or prefer the linear mixed effects model and do a FDR? How do you decide between the two?

Thanks! Swati

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Thanks, Martin. This helps a lot.

Swati

____________________________________________ Swati Rane Levendovszky, PhD Interim Director, Diagnostic Imaging Sciences Center Assistant Professor, Integrated Brain Imaging Center Radiology University of Washington Box 357115 | AA035 HSB | Seattle, WA 98195 srleven@uw.edumailto:srleven@uw.edu | Ph: 206 543 6159 Web: https://sites.google.com/site/uwswatirane/ ____________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Reuter mreuter@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, January 17, 2020 at 3:46 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

Hi Swati,

- yes, you can treat the percent change maps (PC1) as the signal instead of the thickness and do a regular analysis (so either multiple comparisons or sim etc).

- and yes, I would always recommend to use the linear mixed effects model instead as it is specifically designed for longitudinal data. The percent change (2 step approach) is a remainder of the time before we had the LME. Both models are similar only if the longitudinal data has the same number of time points for each subject and if those time points are equally spaced. That is rarely the case and LME can account for that.

Best, Martin

On 17. Jan 2020, at 00:59, Swati Rane <srleven@uw.edumailto:srleven@uw.edu> wrote:

External Email - Use Caution

It is the file computed longitudinal processing that represents the rate with respect to the thickness at the first time point computed by long_mris_slopes.

Swati

____________________________________________ Swati Rane Levendovszky, PhD Interim Director, Diagnostic Imaging Sciences Center Assistant Professor, Integrated Brain Imaging Center Radiology University of Washington Box 357115 | AA035 HSB | Seattle, WA 98195 srleven@uw.edumailto:srleven@uw.edu | Ph: 206 543 6159 Web: https://sites.google.com/site/uwswatirane/ ____________________________________________

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, January 16, 2020 at 3:26 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

Sorry, what is "pc1"? On 1/14/2020 9:44 AM, Swati Rane wrote: External Email - Use Caution Hello,

I was wondering if someone could answer my question below

Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files.

Are there any set of parameters that should be set differently when using pc1 instead of thickness files?

Thanks! Swati

____________________________________________ Swati Rane Levendovszky, PhD Interim Director,Diagnostic Imaging Sciences Center Assistant Professor,Integrated Brain Imaging Center Radiology University of Washington Box 357115 | AA035 HSB | Seattle, WA 98195 srleven@uw.edumailto:srleven@uw.edu | Ph: 206 543 6159 Web: https://sites.google.com/site/uwswatirane/ ____________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Swati Rane srleven@uw.edumailto:srleven@uw.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, January 10, 2020 at 10:06 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

External Email - Use Caution Hello FreeSurfer Developers,

I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you could use the multiple comparisons corrections that come with it but does not comment on using the mri_glmfit-sim option.

I just want to confirm whether there is anything prohibiting me from using mri_glmfit-sim. Are there any set of parameters that should be set differently when using pc-1 instead of thickness files?

Also, would you do a stricter correction and stick to the longitudinal model or prefer the linear mixed effects model and do a FDR? How do you decide between the two?

Thanks! Swati

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer