Dear FreeSurfer users!
I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject.
Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses.
Then I would have to convert from freesurfer space to SPM space via the coordinates.
And - I would also have to convert from .mgz to .nii data format.
Does any have any tips on how to do this? Or a script?
Kind Regards, Anna B. Josefson
use mri_convertcheck this linkhttps://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html
Azeez Adebimpe
Date: Fri, 31 May 2013 13:23:20 +0200 From: anna.b.josefson@gmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Conversion
Dear FreeSurfer users!
I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject.
Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses.
Then I would have to convert from freesurfer space to SPM space via the coordinates.
And - I would also have to convert from .mgz to .nii data format.
Does any have any tips on how to do this? Or a script?
Kind Regards, Anna B. Josefson
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Anna, if you need to get it back into the native anatomical space, see
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
You can use nii as the output format instead of mgz
doug
On 5/31/13 7:23 AM, Anna Josefson wrote:
Dear FreeSurfer users!
I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject.
Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses.
Then I would have to convert from freesurfer space to SPM space via the coordinates.
And - I would also have to convert from .mgz to .nii data format.
Does any have any tips on how to do this? Or a script?
Kind Regards, Anna B. Josefson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi again freesurfers,
I have some beginner's problems.
I want to use some specific cortical and subcortical structures from Recon-all as ROI's in my SPM analyses. How do I extract and save these as binary masks ?
Would this be a good idea: pick the structures I want from here http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferCol... for instance left&right amygdala- + insula
and then do this: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFunct...https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace?highlight=%28space%29%7C%28functional%29
I wonder, what is the meaning of the term "functinal space" - is it native space or in group space?
And can I save individual structures, e.g. amygdala as separate masks?
Best, Anna
---------- Forwarded message ---------- From: Anna Josefson anna.b.josefson@gmail.com Date: 2013/5/31 Subject: Conversion To: freesurfer@nmr.mgh.harvard.edu
Dear FreeSurfer users!
I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject.
Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses.
Then I would have to convert from freesurfer space to SPM space via the coordinates.
And - I would also have to convert from .mgz to .nii data format.
Does any have any tips on how to do this? Or a script?
Kind Regards, Anna B. Josefson
Hi Anna, if you just want to create a binary mask, you can use
mri_binarize --i aparc+aseg.mgz --match 18 54 1035 2035 --o amyg+insula.nii
this will give you a binary mask of amygala and insula
doug
On 6/12/13 10:50 AM, Anna Josefson wrote:
Hi again freesurfers,
I have some beginner's problems.
I want to use some specific cortical and subcortical structures from Recon-all as ROI's in my SPM analyses. How do I extract and save these as binary masks ?
Would this be a good idea: pick the structures I want from here http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferCol... for instance left&right amygdala- + insula
and then do this: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFunct... https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace?highlight=%28space%29%7C%28functional%29
I wonder, what is the meaning of the term "functinal space" - is it native space or in group space?
And can I save individual structures, e.g. amygdala as separate masks?
Best, Anna
---------- Forwarded message ---------- From: *Anna Josefson* <anna.b.josefson@gmail.com mailto:anna.b.josefson@gmail.com> Date: 2013/5/31 Subject: Conversion To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Dear FreeSurfer users!
I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject.
Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses.
Then I would have to convert from freesurfer space to SPM space via the coordinates.
And - I would also have to convert from .mgz to .nii data format.
Does any have any tips on how to do this? Or a script?
Kind Regards, Anna B. Josefson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu