Please ignore my second question. It looks correct in your original email. I must mess up when doing cut and paste.
From: Huang, Yujing Sent: Wednesday, February 22, 2023 9:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] How to calculate the mean FA value in the hippocampus
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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 <YHUANG43@mgh.harvard.edumailto: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_binarizehttps://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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lin Cai Sent: Tuesday, February 21, 2023 9:15 AM To: freesurfer@nmr.mgh.harvard.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1K82V3hWOtrfvPRi7lFTSDKdzDdOqYlaCHTDt0DHlBQtuyB11RC89Blzrr3e4imnpEW7b5taU62LEcfmMe9YIgITmRWitZSBUsCSAI_Uylj2SQLGvRicxJrg0gnFQvfptO_Tt-282tPb-kwXVYNlcyA6wgD1Teptg-GUao-szQP68TzaBDPWLJAO94PPc9cK-x47gqkrgNb04fOAMPK04SzVMYZFkc3etVGtbsDtkKFgBcvJtIzeAJBv09ba7pMoKk1KaN7kkCByZpNYg3_T21bX9B44B_m5TqpmKqVXKNjUqXUOx1y1lIa0MYdUnDzJNIhqf6pobprrf0svsqXj6cg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1kV5GjuHmEIsgX1RCZ8jVZTTZCWv4HX-m2nstb9d3OMf1Abn3H9Fv6uuehNsVmON6nSUNU5KFfqcGSQbKPE3md-qFWQfD3kcN0P6e6vbQAHair8dnn9HVYhjs0bZSBw5PKCU6X5qXo6uJ8NSztrCDSoK09pPwCmqbPGF9QoFzbojJs7MNSECsL-buWJEh3uOjBVLK4eNHJvy_T49N7Quw80lbjdGf1kDx2VHWuFF6NEglnDGE_ngBEgTXH8Eczmzv2Gx-cEbTcbfeV3r3B56BpGAwTyuyJDywc0_Il7r-oy_gWfwyLjzIT3nPcuvvwlNnXvDqzv5hDTybBYy7I8fXbw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1kV5GjuHmEIsgX1RCZ8jVZTTZCWv4HX-m2nstb9d3OMf1Abn3H9Fv6uuehNsVmON6nSUNU5KFfqcGSQbKPE3md-qFWQfD3kcN0P6e6vbQAHair8dnn9HVYhjs0bZSBw5PKCU6X5qXo6uJ8NSztrCDSoK09pPwCmqbPGF9QoFzbojJs7MNSECsL-buWJEh3uOjBVLK4eNHJvy_T49N7Quw80lbjdGf1kDx2VHWuFF6NEglnDGE_ngBEgTXH8Eczmzv2Gx-cEbTcbfeV3r3B56BpGAwTyuyJDywc0_Il7r-oy_gWfwyLjzIT3nPcuvvwlNnXvDqzv5hDTybBYy7I8fXbw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
-- Lin Cai
Project Researcher University of Tokyo, Center for Evolutionary Cognitive Sciences Tokyo, Japan