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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Hello,

You mean the group analysis? we have a lot of choice, in Freesurfer, you can use Qdec or command line, but actually, here, I just do some regression in one group, so it is not really two groups, then I just wanna plot the p value for the correlation into the anatomical image.

For your question, you can use matlab regression function, FS group analysis, or surfstat, you have a lot of choices, but anyway, they are the same.

I will give you some links here:

http://www.math.mcgill.ca/keith/surfstat/

SurfStat - McGill Universityhttp://www.math.mcgill.ca/keith/surfstat/ www.math.mcgill.ca SurfStat A Matlab toolbox for the statistical analysis of univariate and multivariate surface and volumetric data using linear mixed effects models and random field ...

http://freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview FsTutorial/QdecGroupAnalysis_freeview - Free Surfer Wikihttp://freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview freesurfer.net It may take a few seconds for Qdec to open. The ampersand directs the terminal to run this process in the background, so you may see your command prompt return before ...

https://fr.mathworks.com/help/stats/linear-regression.html Linear Regression - MATLAB & Simulink - MathWorks Francehttps://fr.mathworks.com/help/stats/linear-regression.html fr.mathworks.com Multiple, stepwise, multivariate regression models, and more

________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de miracle ozzoude miracooloz@gmail.com Envoyé : mardi 3 janvier 2017 21:26 À : Freesurfer support list Objet : Re: [Freesurfer] View sig map on anatomical volume from volume-based group anaysis

Hey Hao, What software did you use to do your analysis? Also, if you are ok with it, can you please post your scripts on how you did it. I want to implement it in my analysis. Thank you very much. Paul

On Mon, Jan 2, 2017 at 7:52 AM, Hao wen <hao.freesurfer@hotmail.commailto:hao.freesurfer@hotmail.com> 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:

[cid:e4f431a9-4e18-4dec-8275-ce4080b061f2]

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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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.