Hi Yujing,

Thank you very much for your help.

It seems to solve my problem. I can obtain the mean FA value in the left hippocampus.

But I found another issue on the order of processing data.

# order 1: I first aligned the aparc+aseg.mgz to the FA.nii.gz, and then created the hippocampus mask.

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

mri_convert nu.mgz nu.nii.gz

flirt -in nu.nii.gz -ref FA.nii.gz -omat f2d.mat

flirt -in aparc+aseg.nii.gz -ref FA.nii.gz -applyxfm -init f2d.mat -out aparc+aseg_diffspace.nii.gz

mri_convert aparc+aseg_diffspace.nii.gz aparc+aseg_diffspace.mgz

mri_binarize --i aparc+aseg_diffspace.mgz --o left_hippocampus.mgz --match 17

mri_convert left_hippocampus.mgz left_hippocampus.nii.gz

fslstats FA.nii.gz -k left_hippocampus.nii.gz -M

# order 2: I first created the hippocampus mask, and then directly aligned this mask to FA.nii.gz.

mri_binarize --i aparc+aseg.mgz --o left_hippocampus.mgz --match 17

mri_convert left_hippocampus.mgz left_hippocampus.nii.gz

flirt -in nu.nii.gz -ref FA.nii.gz -omat f2d.mat

flirt -in left_hippocampus.nii.gz -ref FA.nii.gz -applyxfm -init f2d.mat -out left_hippocampus_diffspace.nii.gz

fslstats FA.nii.gz -k left_hippocampus_diffspace.nii.gz -M

Using the two methods above mentioned, I found mean FA values derived from fslstats are different.

Do you have any thoughts on this?

Thank you very much in advance.

Lin

On Tue, Feb 21, 2023 at 11:57 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

Hi Lin,

You can try mri_binarize to obtain the mask - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize

FreeSurferColorLUT.txt in your Freesurfer install directory will give you a complete list of aparc/aseg labels.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lin Cai
Sent: Tuesday, February 21, 2023 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to calculate the mean FA value in the hippocampus

External Email - Use Caution

Dear Freesurfer experts,

I want to calculate the mean FA value in the hippocampus.

Now I have already obtained the FA map for the whole brain in the native space.

And I have the aparc+aseg.mgz file after running the recon -all analysis.

Does someone know how to use freesurfer functions to obtain the hippocampus mask according to the DK atlas? I want to use this mask to calculate the mean FA value in the hippocampus.

Best regards,

Lin

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