If you have a value for a given ROI, you can do something like this in matlab
seg = MRIread('aparc+aseg.mgz');
overlay = seg;
overlay.vol = zeros(size(overlay.vol));
HippocampusIndex = find(seg.vol == 17); % 17 from $FREESURFER_HOME/FreeSurferColorLUT.txt
overlay.vol(HippocampusIndex) = YourValueForLeftHippocampus
MRIwrite(overlay,'overlay.nii.gz');
You can then visualize overlay.nii.gz on the anatomy. If you want multiple ROIs in the same volume, then just fill in the missing data.
On 01/02/2017 07:52 AM, Hao wen wrote:
Hello:
I have a question, after recon-all, I did some group analysis with the aseg.stats( not surface-based), so my question is :
Does freesurfer has some volume-based group analysis(not for fMRI) for plotting the significance map, I searched google, and wanna some results like this:
I know here is for fMRI-sMRI based analysis:
So i want to map some values for the subcortical structures in the anatomical image, but for the command here, how can I get the sig.nii(right now, we just have the result p-value for every subcortical structures), I know in FS, we can use mri_glmfit to have the significance map
Any advice will be appreciated
Hao
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