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Typo
yhat = X(:,[1 2 3])*beta([1 2 3],:)
On 5/21/2020 2:12 PM, Hua, Jessica wrote:
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I apologize for resending all of this info, but my email is acting up
and every time I try to respond to the other email, my Outlook freezes.
Here is info from our
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I apologize for resending all of this info, but my email is acting up and every
time I try to respond to the other email, my Outlook freezes.
Here is info from our thread. I modified it to include the analysis in which I
found significant clusters
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Attached are the fsgd and Xg.dat files.
---
Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
GroupComparison_AllMRI.AgeSexICV.fsgd
Description: GroupComparison_AllMRI.AgeSexICV.fsgd
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I was not sure how to modify the last line in your code in order to calculate
adjusted values accounting for age, sex, and ICV for each participant (this is
a three group design).
Your code:
There is not an easy way to do it, but you can do it in
And what is your new question?
On 5/17/20 12:10 PM, Hua, Jessica wrote:
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Sure, attached are the files again and here is our previous
correspondence:
Original question:
After running the permutation and finding significant clusters, I am
trying to
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Sure, attached are the files again and here is our previous correspondence:
Original question:
After running the permutation and finding significant clusters, I am trying to
calculate the value for each participant for these significant clusters.
Sorry, can you include previous correspondence so that I have context?
On 5/16/2020 1:55 PM, Hua, Jessica wrote:
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Sure, attached is the FSGD file. In case helpful, I have also attached
the Xg.dat file.
---
Jessica Hua, M.A.
Cognitive and Emotional
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Sure, attached is the FSGD file. In case helpful, I have also attached the
Xg.dat file.
---
Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
GroupComparison_AllMRI.AgeSexICV.fsgd
There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[i j k ...]*beta([i j k ...])
where i j k ... indicate the factors you want keep in your data. Each
factor gets a column in the
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After running the permutation and finding significant clusters, I am trying to
calculate the value for each participant for these significant clusters.
The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the
adjusted values
That is how you would compute a partial model fit, though I'm not sure
which part of the model you are trying to fit. In what you have, it will
remove the main effect of group (but not interactions).
On 5/14/2020 1:30 PM, Hua, Jessica wrote:
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Hi
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Hi FreeSurfer Experts,
I am trying to extract or calculate the adjusted values for each participant in
each cluster after accounting for covariates in my permutation analysis.
This is a 3 group analysis with 3 covariates (age, sex, and ICV).
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;
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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
The value in the ocn.dat file totally depends on what you used as input
(--y) to mri_glmfit. If you used thickness, then it is thickness. That
mri_segstats command is almost correct. You will need to add
--accumulate so that it gives you the total volume rather than the average
On 06/13/2018
On 06/11/2018 11:07 PM, Hua, Jessica wrote:
>
>
> Dear Freesurfer Experts:
>
>
> I analyzed my data following the guidelines on the FSL 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
>
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Dear Freesurfer Experts:
I analyzed my data following the guidelines on the FSL 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.
I set
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