On 6/21/2021 12:13 PM, Yu-Wei Chang wrote:

External Email - Use Caution

External Email - Use Caution

Dear PetSurfer and Freesurfer Developers,

I would like to run partial volume corrections on amyloid PET images (from ADNI) with PetSurfer.

I have downloaded the amyloid PET images that were intensity normalized to the cerebellar GM.

However, I noticed that the PVC analysis in PetSurfer uses the Pons as a reference region.

I don't have much experience with PET analyses but I was wondering

1.1 If I should use the same reference region for the PVC?

This is a biological question, not a technical one. If they used cerebellum, probably good to stick with that

1.2 If so, how can I change the Pons for the Cerebellar GM in the commands on the website?

I found a similar question raised in the forum (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52918.html) and the provided solution is to add ‘--rescale 7 8 46 47’ for left and right cblum wm and gm.

2.1 Does ‘--rescale 7 8 46 47’ suit my question 1?

Yes

2.2 If so, where can I find the whole list of ids that specify every brain region in the left and right hemispheres?

Look in gtmseg.ctab in $SUBJECTS_DIR/subject/mri

Thank you.

Best,

Yu-Wei

****************************

Yu-Wei Chang 張育瑋

Doctoral student

UNIVERSITY OF GOTHENBURG

Department of Physics

Gothenburg, Sweden

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