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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 - https://secure-web.cisco.com/1cXC2iiVT1KDP6BU7HZdfBZX6-FK3STwZQDnz8lAacrrrXw...
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,
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