Hi Lin,
I’m not sure why the results are different.
The input/output volumes for mri_binarize can be either mgz or nii.gz. With
your first method, can you try to convert aparc+aseg_diffspace.nii.gz to
left_hippocampus.nii.gz directly?
Also your second to last command ‘mri_convert left_hippocampus.mgz
aparc+aseg_diffspace.mgz’, is it a typo?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Lin Cai
Sent: Wednesday, February 22, 2023 12:46 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to calculate the mean FA value in the hippocampus
External Email - Use Caution
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 aparc+aseg_diffspace.mgz
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
<yhuan...@mgh.harvard.edu<mailto:yhuan...@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<https://secure-web.cisco.com/1cXC2iiVT1KDP6BU7HZdfBZX6-FK3STwZQDnz8lAacrrrXwsWKgD7xvH8bjW6v7IfK4DPrXaZ6qRgvkxpctH8WhHCb4FjsdkomaWP8so_aQlOUnLsNFnxTtAl5uqGOulEEhR5q0QCMaPepo0B5f-PNPUdDlSNg2IxIztJu2W088S-WAsX47sWQr3QA1Q02Ek9nDIVIXLPJ-Pd5tOuj-Fe7ugW33aOUMD5KyBdxlKMevm9pVCw_XJLuPEVPXYYjdai0LJxsoC9R6SrZHkE1xtvKV1m-iv54XD5wTdFDim_Ysg_VbA2Emg-GxbIHfMiKZQTev0XxNJt6tJO7oUiVoTMug/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_binarize>
FreeSurferColorLUT.txt in your Freesurfer install directory will give you a
complete list of aparc/aseg labels.
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Lin Cai
Sent: Tuesday, February 21, 2023 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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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--
Lin Cai
Project Researcher
University of Tokyo, Center for Evolutionary Cognitive Sciences
Tokyo, Japan
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