sorry for the delay. There is not a super easy way to do this, but it is possible in matlab. cd into the glmdir folder and start matlab, then

X = load('Xg.dat');

beta = MRIread('beta.mgh');

betamat = fast_vol2mat(beta);

yhatmat = X(:,[i j k m n])*betamat([i j k m n],:);

yhat = beta;

yhat.vol = fast_mat2vol(yhat,yhat.volsize);

MRIwrite(yhat,'yhat.ijkmn.mgh');

The key here is that you need to select the covariates (i j k m n) that you want to include. Each one will form a column in the design matrix and will have an element in the beta. By selecting the components you want, you exclude the ones you don't want. this simple formulation won't work if a given component spans both a factor of interest and a nuisance factor (eg, Male-AD when you want remove the effects of gender). But there is a way around this too. let me know.

On 6/24/18 9:58 AM, Hua, Jessica wrote:

Hi FreeSurfer experts,

Just bringing this question back up to the top: I analyzed my data following the guidelines on the FreeSurfer Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the significant clusters for each of my participants.

Is there a way to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates (age, sex, and ICV)?

Best,

Jessica

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Today's Topics:

1. FreeSurfer Manual Edit Sequence (David S Lee)    2. Using grad_unwarp (James Gullickson)

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Message: 1 Date: Fri, 22 Jun 2018 11:37:44 -0500 From: David S Lee david.s.lee@wisc.edu Subject: [Freesurfer] FreeSurfer Manual Edit Sequence To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGcZjx8px96eS=O64q5nivBObJP9cqDha3_R87G3GHdjkVQnqA@mail.gmail.com Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hello Experts,

When performing manual edits on brain masks, white matter, and gray matter, do I have to strictly follow the sequences(process stages) listed here https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all?

For instance, the link suggests that "autorecon2-pial is used after editing brain volume *after running -autorecon2".

In other words, is it okay to perform "autorecon2-pial" before "autorecon2-wm"?

Thank you for your time,

David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115