External Email - Use Caution
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?
‘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
External Email - Use Caution 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?
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
External Email - Use Caution
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?
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
* External Email - Use Caution *
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?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Sorry for the oversight
Thank you, Best Wishes. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Monday, June 24, 2024 9:52 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Calculating intensity of Individual voxel
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU Sent: Friday, June 21, 2024 7:46 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Calculating intensity of Individual voxel
External Email - Use Caution
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?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
When I tried this , I got 0.00000. I have attached a screenshot of it.
[image: image.png]
On Fri, Jun 21, 2024 at 2:47 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
‘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
External Email - Use Caution *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? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 https://www.massgeneralbrigham.org/complianceline < https://www.massgeneralbrigham.org/complianceline%3E .
Replace [c r s] with voxel coordinates that you are interested in.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Tuesday, July 2, 2024 2:52 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Calculating intensity of Individual voxel
External Email - Use Caution When I tried this , I got 0.00000. I have attached a screenshot of it.
[cid:image001.png@01DACC90.A62265C0]
On Fri, Jun 21, 2024 at 2:47 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: ‘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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Calculating intensity of Individual voxel
External Email - Use Caution 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? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 https://www.massgeneralbrigham.org/complianceline https://www.massgeneralbrigham.org/complianceline .
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
ERNEST KISSI -
Gaurav Ambwani -
Huang, Yujing