Thank you Dr Bruce,

I want to calculate PET signal in each Brodman map! I will give an example:

If I want to caclulate PET singal for every parcellate and segment in the atlas "wmparc.mgz". I do the following:

bbregister --t1 --mov T1.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID

mri_vol2vol --mov PET_MAP.nii --reg t1.reg.dat --fstarg --interp nearest --o PET_MAP.anat.nii
mri_segstats --seg $SUBJECTS_DIR/SUBJID/mri/wmparc.mgz --ctab-default --i PET_MAP.anat.nii --mask PET_MAP.anat.nii --sum PET_MAP.summary.dat

How can I do the same previous steps ( if correct) on the atlas V1. I.e how can I replace the atalas "wmparc" in the command "mri_segstat" with the atals V1 to get PET signal for every brodman?

Bests,
John

Sent: Wednesday, May 11, 2016 at 8:10 PM
From: "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] V1 Atlas ( brodman maps)

Hi John

recon-all should create lh.BA.annot and rh.BA.annot parcellations that
contain all the Brodmann areas we know how to label

cheers
Bruce

On Thu, 12 May 2016, John Anderson wrote:

> Dear experts,
> I want to use the atlas V1 to calculate PET signal for Brodman areas. How
> can I create this atlas in the form of “aseg.mgz” or ”wmparc.mgz” ( i.e all
> the BAs in one file) to feed it in the command “mri-segstat”?
> Bests,
> John
>
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