I don't think she was responding to your question but rather to that of Ernest

On 6/21/2024 1:23 PM, Gaurav Ambwani wrote:

        External Email - Use Caution        

Dear Yujing, 

I don't think that this was my question. Here are the contents of what I sent in my previous email:

I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain extraction tool in 3D slicer, and then I registered it in fsl to a skull stripped version of a T1 weighted image of a Stroke patient (which I got from Openneuro). 

The purpose of doing this is to, get the aseg.mgz file and overlay that onto the MRI of the stroke patient. 

Previously I have taken the T1 1mm MNI image and received an aseg.mgz file which I have overlayed onto my MNI registered T1 weighted stroke MRI and that worked perfectly. However, This time I have taken the T1 1mm MNI image registered that to my stroke T1 MRI, and the registered image hasn't gone through freesurfer. 

I have attached the recon-all.log file in this email. 

Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Distributor ID: Ubuntu
Description:    Ubuntu 22.04.4 LTS
Release:        22.04
Codename:       jammy

I am using a WSL in windows 11 (64 bit)

Thank you, 
Best Wishes, 
Gaurav Ambwani.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Sent: Friday, June 21, 2024 7:46 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Calculating intensity of Individual voxel
 

‘mri_info vol.mgz --voxel c r s’ will print the voxel value from col row slice of all frames.

 

Best,

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI
Sent: Friday, June 21, 2024 5:16 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Calculating intensity of Individual voxel

 

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Hi, freesurfer team

 

Is there a way to calculate the intensity of a voxel.Let say, I have a voxel with coordinate 20, 30 and 34 and I wanna know the intensity of it. Can it be done in freesurfer?


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