Dear Freesurfer experts,
I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I am going through the following steps to get the MNI coordinates of the regions:
1. Morph the subject's brain to fslaverage;
2. Load the inflated surface of fslaverage to MNE analyze;
3. Look for regions that are activated during my task;
3. Use view>show coordinates to show the coordinates of the vertex;
4. The surface RAS (MRI) coordinates are shown;
5. Used these coordinates as MNI coordinates.
Because I was using SPM in the past and am quite new to freesurfer, I strongly hope someone can help me to check if I have done it correctly. Thank you so much for your help!
Best wishes, Baojuan
Hi Baojuan, that coordinate will be mni305 space. Is that what you want?
On 07/06/2016 04:17 PM, Li, Baojuan wrote:
Dear Freesurfer experts,
I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I am going through the following steps to get the MNI coordinates of the regions:
Morph the subject's brain to fslaverage;
Load the inflated surface of fslaverage to MNE analyze;
Look for regions that are activated during my task;
Use view>show coordinates to show the coordinates of the vertex;
The surface RAS (MRI) coordinates are shown;
Used these coordinates as MNI coordinates.
Because I was using SPM in the past and am quite new to freesurfer, I strongly hope someone can help me to check if I have done it correctly. Thank you so much for your help!
Best wishes, Baojuan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thank you so much! Because I will do the analysis using SPM, I need the coordinates in MNI152 space. I found a transformation between them:
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] Is this transformation correct? I guess I can then get the MNI152 coordinates in this way:
P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Am I correct?
Best wishes, Baojuan
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 4:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslaverage/MNI coordinates
Hi Baojuan, that coordinate will be mni305 space. Is that what you want?
On 07/06/2016 04:17 PM, Li, Baojuan wrote:
Dear Freesurfer experts,
I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I am going through the following steps to get the MNI coordinates of the regions:
Morph the subject's brain to fslaverage;
Load the inflated surface of fslaverage to MNE analyze;
Look for regions that are activated during my task;
Use view>show coordinates to show the coordinates of the vertex;
The surface RAS (MRI) coordinates are shown;
Used these coordinates as MNI coordinates.
Because I was using SPM in the past and am quite new to freesurfer, I strongly hope someone can help me to check if I have done it correctly. Thank you so much for your help!
Best wishes, Baojuan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I've just added your use case to this page. See Case 8. http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 07/06/2016 05:09 PM, Li, Baojuan wrote:
Hi Doug,
Thank you so much! Because I will do the analysis using SPM, I need the coordinates in MNI152 space. I found a transformation between them:
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] Is this transformation correct? I guess I can then get the MNI152 coordinates in this way:
P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Am I correct?
Best wishes, Baojuan
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 4:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslaverage/MNI coordinates
Hi Baojuan, that coordinate will be mni305 space. Is that what you want?
On 07/06/2016 04:17 PM, Li, Baojuan wrote:
Dear Freesurfer experts,
I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I am going through the following steps to get the MNI coordinates of the regions:
Morph the subject's brain to fslaverage;
Load the inflated surface of fslaverage to MNE analyze;
Look for regions that are activated during my task;
Use view>show coordinates to show the coordinates of the vertex;
The surface RAS (MRI) coordinates are shown;
Used these coordinates as MNI coordinates.
Because I was using SPM in the past and am quite new to freesurfer, I strongly hope someone can help me to check if I have done it correctly. Thank you so much for your help!
Best wishes, Baojuan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you so much! ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, July 07, 2016 1:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslaverage/MNI coordinates
I've just added your use case to this page. See Case 8. http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 07/06/2016 05:09 PM, Li, Baojuan wrote:
Hi Doug,
Thank you so much! Because I will do the analysis using SPM, I need the coordinates in MNI152 space. I found a transformation between them:
M = [ 0.9975 -0.0073 0.0176 -0.0429 0.0146 1.0009 -0.0024 1.5496 -0.0130 -0.0093 0.9971 1.1840 0 0 0 1.0000] Is this transformation correct? I guess I can then get the MNI152 coordinates in this way:
P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305
Am I correct?
Best wishes, Baojuan
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 4:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslaverage/MNI coordinates
Hi Baojuan, that coordinate will be mni305 space. Is that what you want?
On 07/06/2016 04:17 PM, Li, Baojuan wrote:
Dear Freesurfer experts,
I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I am going through the following steps to get the MNI coordinates of the regions:
Morph the subject's brain to fslaverage;
Load the inflated surface of fslaverage to MNE analyze;
Look for regions that are activated during my task;
Use view>show coordinates to show the coordinates of the vertex;
The surface RAS (MRI) coordinates are shown;
Used these coordinates as MNI coordinates.
Because I was using SPM in the past and am quite new to freesurfer, I strongly hope someone can help me to check if I have done it correctly. Thank you so much for your help!
Best wishes, Baojuan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Li, Baojuan