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Hi Anastasia,

Thank you for your reply. So for segmentation.stats, should I divide the regional areas by eTIV or treat it as a covariate for a group comparison? Is it the same with Total cerebral white matter volume for wmparc.stats. For Diffusion measurement, for example, FA, if a subject has lower FA in general in the brain, should I adjust the whole brain FA or average FA for that matter?

Best, Qi

On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:

Hi Qi - Correcting for overall brain size is important when you are comparing measures of length/area/volume. As in, you want to know if a region specifically is bigger in population A vs. B, and not just because the whole brain is bigger. In that case, use eTIV (estimated total intracranial volume) from the freesurfer segmentation stats.

FA is not measuring size of a region, so correcting for brain size is less of an issue there. It's a possibility perhaps that for someone with a substantially smaller brain there may be more partial voluming affecting FA, so it can't hurt to check for an effect before including it in your analysis.

Anastasia.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Monday, August 31, 2020 11:44 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] group level analysis

    External Email - Use Caution

Hi,

When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA? Thank you so much!

Best, Qi

---

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

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Hi Anastasia,

Thank you for the clarification! As you said, if I regress out the global FA, I could wipe out the regional FA. But what if my question is to find out exactly which regional FA differentiate the two groups rather than if global FA is different between groups. In that case, should I control the global FA when running regional FA between groups?

Best, Qi

On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or surface area measures.

In a situation where a regional FA difference is high enough to also cause a whole brain FA difference, regressing out the latter could wipe out the former. Not sure why you'd want to do that, unless there's a specific question you want to ask that requires it.

Anastasia.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Monday, August 31, 2020 10:03 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] group level analysis

    External Email - Use Caution

Hi Anastasia,

Thank you for your reply. So for segmentation.stats, should I divide the regional areas by eTIV or treat it as a covariate for a group comparison? Is it the same with Total cerebral white matter volume for wmparc.stats. For Diffusion measurement, for example, FA, if a subject has lower FA in general in the brain, should I adjust the whole brain FA or average FA for that matter?

Best, Qi

On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Qi - Correcting for overall brain size is important when you are comparing measures of length/area/volume. As in, you want to know if a region specifically is bigger in population A vs. B, and not just because the whole brain is bigger. In that case, use eTIV (estimated total intracranial volume) from the freesurfer segmentation stats.

FA is not measuring size of a region, so correcting for brain size is less of an issue there. It's a possibility perhaps that for someone with a substantially smaller brain there may be more partial voluming affecting FA, so it can't hurt to check for an effect before including it in your analysis.

Anastasia.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Monday, August 31, 2020 11:44 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] group level analysis

    External Email - Use Caution

Hi,

When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA? Thank you so much!

Best, Qi

---

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

--

Ph.D. candidate Icahn School of Medicine at Mount Sinai

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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.

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Now I see. Thank you very much and have a good night!

Best, Qi

On Mon, Aug 31, 2020 at 11:12 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Let me put it this way. It's possible that your amygdala is bigger than mine without your brain overall being bigger than mine. But if your corpus callosum has higher average FA than mine, then your brain overall will have higher average FA than mine (assuming we don't have a reverse difference somewhere else). Higher average whole-brain FA doesn’t mean that the FA is higher *everywhere* in the brain, so it's not a global effect in the way that a bigger brain would be a global effect. I hope this makes sense!

---

*From:* Zeng, Qi qi.zeng@icahn.mssm.edu *Sent:* Monday, August 31, 2020 10:57 PM *To:* Yendiki, Anastasia AYENDIKI@mgh.harvard.edu *Cc:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] group level analysis

    External Email - Use Caution

Hi Anastasia,

Thank you for the clarification! As you said, if I regress out the global FA, I could wipe out the regional FA. But what if my question is to find out exactly which regional FA differentiate the two groups rather than if global FA is different between groups. In that case, should I control the global FA when running regional FA between groups?

Best, Qi

On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or surface area measures.

In a situation where a regional FA difference is high enough to also cause a whole brain FA difference, regressing out the latter could wipe out the former. Not sure why you'd want to do that, unless there's a specific question you want to ask that requires it.

Anastasia.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Monday, August 31, 2020 10:03 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] group level analysis

    External Email - Use Caution

Hi Anastasia,

Thank you for your reply. So for segmentation.stats, should I divide the regional areas by eTIV or treat it as a covariate for a group comparison? Is it the same with Total cerebral white matter volume for wmparc.stats. For Diffusion measurement, for example, FA, if a subject has lower FA in general in the brain, should I adjust the whole brain FA or average FA for that matter?

Best, Qi

On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Qi - Correcting for overall brain size is important when you are comparing measures of length/area/volume. As in, you want to know if a region specifically is bigger in population A vs. B, and not just because the whole brain is bigger. In that case, use eTIV (estimated total intracranial volume) from the freesurfer segmentation stats.

FA is not measuring size of a region, so correcting for brain size is less of an issue there. It's a possibility perhaps that for someone with a substantially smaller brain there may be more partial voluming affecting FA, so it can't hurt to check for an effect before including it in your analysis.

Anastasia.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Monday, August 31, 2020 11:44 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] group level analysis

    External Email - Use Caution

Hi,

When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA? Thank you so much!

Best, Qi

---

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

--

Ph.D. candidate Icahn School of Medicine at Mount Sinai

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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.

--

Ph.D. candidate Icahn School of Medicine at Mount Sinai