External Email - Use Caution
Thanks! I will try it.
Kind Regards,
Andy (Junghyun) Kim
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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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