Thanks very much, that is what i want exactly, actually, I also tried to created a customized LUT and just assign the ROIs specific color and make other region to be white, It works, but It can not give me the color bar to define the magnitude of my p values, I will try your way, actually, this is what I did for the thickness mapping:)
Thanks
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas N Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 3 janvier 2017 21:11 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] View sig map on anatomical volume from volume-based group anaysis
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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