Good afternoon all,
I was hoping to get some advice on how to approach this. Any and all feedback is much appreciated.
My group has been using FSL’s Feat to run analyses for our PET-MR project. Part of what we need to do next is create masks using fslmaths that overlay the significant clusters in the zstat images with different brain regions. We then extract standard uptake values (SUVs) from the clusters in each region for each subject so that we can graph them. The issue is that the Atlas in FSL is the Harvard-Oxford Cortical Structural Atlas, which has a broader parcellation of the cingulate cortex then we would like to use (just anterior/posterior).
Is there any way to use the Desterieux atlas with FSL? Or any way to do this same kind of analysis with Freesurfer?
I would really appreciate the help.
Best,
Hannah
-- Hannah Bues (she/her) Clinical Research Coordinator - VanElzakker Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital/Harvard Medical School 149 13th Street, Charlestown, MA 02129 Office: (617) 726-8120
I think all you have to do is convert the aparc.a2009s+aseg.mgz to nifti (mri_convert something.mgz something.nii.gz
On 3/20/2023 4:50 PM, Bues, Hannah Francesca wrote:
Good afternoon all,
I was hoping to get some advice on how to approach this. Any and all feedback is much appreciated.
My group has been using FSL’s Feat to run analyses for our PET-MR project. Part of what we need to do next is create masks using fslmaths that overlay the significant clusters in the zstat images with different brain regions. We then extract standard uptake values (SUVs) from the clusters in each region for each subject so that we can graph them. The issue is that the Atlas in FSL is the Harvard-Oxford Cortical Structural Atlas, which has a broader parcellation of the cingulate cortex then we would like to use (just anterior/posterior).
Is there any way to use the Desterieux atlas with FSL? Or any way to do this same kind of analysis with Freesurfer?
I would really appreciate the help.
Best,
Hannah
--
Hannah Bues (she/her)
Clinical Research Coordinator - VanElzakker Lab
Martinos Center for Biomedical Imaging
Massachusetts General Hospital/Harvard Medical School
149 13th Street, Charlestown, MA 02129
Office: (617) 726-8120
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you so much Doug!
Just to clarify, is aparc.a2009s+aseg.mgz in an individual subject’s output folder subject-specific? Ideally, I’d like this parcellation for an MNI brain because that’s what the PET data is registered to. Would /usr/local/freesurfer/stable5_3_0/subjects/cvs_avg35_inMNI152/mri/aparc.a2009s+aseg.mgz be what I’m looking for then?
Best,
Hannah
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Date: Monday, March 27, 2023 at 10:54 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using the Desterieux Cortical Atlas to Extract PET SUVs I think all you have to do is convert the aparc.a2009s+aseg.mgz to nifti (mri_convert something.mgz something.nii.gz On 3/20/2023 4:50 PM, Bues, Hannah Francesca wrote: Good afternoon all,
I was hoping to get some advice on how to approach this. Any and all feedback is much appreciated.
My group has been using FSL’s Feat to run analyses for our PET-MR project. Part of what we need to do next is create masks using fslmaths that overlay the significant clusters in the zstat images with different brain regions. We then extract standard uptake values (SUVs) from the clusters in each region for each subject so that we can graph them. The issue is that the Atlas in FSL is the Harvard-Oxford Cortical Structural Atlas, which has a broader parcellation of the cingulate cortex then we would like to use (just anterior/posterior).
Is there any way to use the Desterieux atlas with FSL? Or any way to do this same kind of analysis with Freesurfer?
I would really appreciate the help.
Best,
Hannah
-- Hannah Bues (she/her) Clinical Research Coordinator - VanElzakker Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital/Harvard Medical School 149 13th Street, Charlestown, MA 02129 Office: (617) 726-8120
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Yes, that should work. It does use a different registration technique (assuming you're not using CVS), but it is probably pretty close
On 3/27/2023 11:59 AM, Bues, Hannah Francesca wrote:
Thank you so much Doug!
Just to clarify, is aparc.a2009s+aseg.mgz in an individual subject’s output folder subject-specific? Ideally, I’d like this parcellation for an MNI brain because that’s what the PET data is registered to. Would /usr/local/freesurfer/stable5_3_0/subjects/cvs_avg35_inMNI152/mri/aparc.a2009s+aseg.mgz be what I’m looking for then?
Best,
Hannah
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Monday, March 27, 2023 at 10:54 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Using the Desterieux Cortical Atlas to Extract PET SUVs
I think all you have to do is convert the aparc.a2009s+aseg.mgz to nifti (mri_convert something.mgz something.nii.gz
On 3/20/2023 4:50 PM, Bues, Hannah Francesca wrote:
Good afternoon all, I was hoping to get some advice on how to approach this. Any and all feedback is much appreciated. My group has been using FSL’s Feat to run analyses for our PET-MR project. Part of what we need to do next is create masks using fslmaths that overlay the significant clusters in the zstat images with different brain regions. We then extract standard uptake values (SUVs) from the clusters in each region for each subject so that we can graph them. The issue is that the Atlas in FSL is the Harvard-Oxford Cortical Structural Atlas, which has a broader parcellation of the cingulate cortex then we would like to use (just anterior/posterior). Is there any way to use the Desterieux atlas with FSL? Or any way to do this same kind of analysis with Freesurfer? I would really appreciate the help. Best, Hannah -- Hannah Bues (she/her) Clinical Research Coordinator - VanElzakker Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital/Harvard Medical School 149 13th Street, Charlestown, MA 02129 Office: (617) 726-8120 _______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
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Bues, Hannah Francesca -
Douglas N. Greve