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Dear FreeSurfer developers,
Hi. I've always appreciated your help.
I am writing this email to kindly ask you how to create a functional ROI where activation (which is a result of FS-FAST) is peak. In volume-based analysis, people often make a "3mm-sphere" seed around peak activation for connectivity analysis. But since it is surface based, there is no "3mm-sphere". Then what would it be for surface?
I tried: mri_surfcluster --in ./masked_sig1.nii.gz --hemi lh --subject fsaverage --thmin 5 --sum ./summary1.txt, but its output is not actually what I want. It tells peak X, Y, Z coordinates, but I want a fixed size of small cluster (like 3mm-sphere in volume) for creating a ROI in different masks (like peak ROI in V1, peak ROI in V2, etc). In addition, minimum threshold may be diffrent depending on masks. By this I mean, if I choose thmin of 5 for both V1 and V2, V1 may have a huge cluster where vertices have values greater than 5, where as V2 may have a small cluster. I just want to get a fixed size of ROI around "peak".
How should I make a functional ROI around peak activation on surface?
Kind Regards, Andy (Junghyun) Kim
If you know what the vertex number is, you can do something like mri_volsynth --dim-surf fsaverage/surf/lh.white --pdf delta --delta-crsf vertexno 0 0 0 --o delta.mgh mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh mri_binarize --i delta.sm3.mgh --min 0.5 --o delta.sm3.bin.mgh delta.sm3.bin.mgh will be a binary disk approximately 3mm in radius
On 4/4/2023 7:24 AM, Andy Kim wrote:
External Email - Use Caution
Dear FreeSurfer developers,
Hi. I've always appreciated your help.
I am writing this email to kindly ask you how to create a functional ROI where activation (which is a result of FS-FAST) is peak. In volume-based analysis, people often make a "3mm-sphere" seed around peak activation for connectivity analysis. But since it is surface based, there is no "3mm-sphere". Then what would it be for surface?
I tried: mri_surfcluster --in ./masked_sig1.nii.gz --hemi lh --subject fsaverage --thmin 5 --sum ./summary1.txt, but its output is not actually what I want. It tells peak X, Y, Z coordinates, but I want a fixed size of small cluster (like 3mm-sphere in volume) for creating a ROI in different masks (like peak ROI in V1, peak ROI in V2, etc). In addition, minimum threshold may be diffrent depending on masks. By this I mean, if I choose thmin of 5 for both V1 and V2, V1 may have a huge cluster where vertices have values greater than 5, where as V2 may have a small cluster. I just want to get a fixed size of ROI around "peak".
How should I make a functional ROI around peak activation on surface?
Kind Regards, Andy (Junghyun) Kim
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks! I will try it.
Kind Regards, Andy (Junghyun) Kim ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, April 6, 2023 11:43 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to create a functional ROI on surface where activation is peak?
If you know what the vertex number is, you can do something like mri_volsynth --dim-surf fsaverage/surf/lh.white --pdf delta --delta-crsf vertexno 0 0 0 --o delta.mgh mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh mri_binarize --i delta.sm3.mgh --min 0.5 --o delta.sm3.bin.mgh delta.sm3.bin.mgh will be a binary disk approximately 3mm in radius
On 4/4/2023 7:24 AM, Andy Kim wrote:
External Email - Use Caution
Dear FreeSurfer developers,
Hi. I've always appreciated your help.
I am writing this email to kindly ask you how to create a functional ROI where activation (which is a result of FS-FAST) is peak. In volume-based analysis, people often make a "3mm-sphere" seed around peak activation for connectivity analysis. But since it is surface based, there is no "3mm-sphere". Then what would it be for surface?
I tried: mri_surfcluster --in ./masked_sig1.nii.gz --hemi lh --subject fsaverage --thmin 5 --sum ./summary1.txt, but its output is not actually what I want. It tells peak X, Y, Z coordinates, but I want a fixed size of small cluster (like 3mm-sphere in volume) for creating a ROI in different masks (like peak ROI in V1, peak ROI in V2, etc). In addition, minimum threshold may be diffrent depending on masks. By this I mean, if I choose thmin of 5 for both V1 and V2, V1 may have a huge cluster where vertices have values greater than 5, where as V2 may have a small cluster. I just want to get a fixed size of ROI around "peak".
How should I make a functional ROI around peak activation on surface?
Kind Regards, Andy (Junghyun) Kim
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freesurfer@nmr.mgh.harvard.edu
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Andy Kim -
Douglas N. Greve