Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 18 May '20

18 May '20

External Email - Use Caution 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 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 design matrix (and a beta). If you need help figuring this out, send the fsgd file. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask
by Elena Pozzi 18 May '20

18 May '20

External Email - Use Caution Hi Douglas, I added some control points, but also and mostly made edits meant to fix the mask (e.g., deleted some voxels).

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vol2subfield single time course from multiple regions
by stdp82＠virgilio.it 18 May '20

18 May '20

External Email - Use Caution Hi list, vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sf ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gz extracts the time course from each thalamic subregions. If I would like to merge multiple regions (e.g. --id 8115 --id 8116) and extract a single time course from them, which is the way? Thanks Stefano

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rh postcentral gyrus segmentation error
by KennethSPrice 18 May '20

18 May '20

External Email - Use Caution Hello Freesurfer Experts! I am looking for some guidance on improving the pial surface estimation at the right post-central gyrus. Looking at the aparc+aseg file, it is clear that the pial surface estimation missed some cortex. I have already experimented with different -wthresh values. Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Get Freesurfer versions 4 and 5
by Ian 18 May '20

18 May '20

External Email - Use Caution Hi freesurfers, Is it possible to download freesurfer versions 4 and 5? Thanks, Ian -- *Ian Hardingham*

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Longitudinal edits on norm.mgz instead of brainmask
by Elena Pozzi 17 May '20

17 May '20

External Email - Use Caution Dear experts, I have a longitudinal study with 2 time points and I created the base template following the longitudinal tutorial. I open the images to inspect the result and I made some edits to the base. However, I made the edits on the norm.mgz image instead of the brainmask.mgz. I suspect this is not right. Is there any way to transfer the edits when I re-run recon-all before creating the longitudinal runs? Or do I have to do all the edits again? Thank you very much in advance.

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 17 May '20

17 May '20

External Email - Use Caution 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. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age, sex, and ICV (this is a three group design). What would be the best way of calculating that? Your response: 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 design matrix (and a beta). If you need help figuring this out, send the fsgd file. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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DTI and T1 AND T2 WEIGHTED IMAGES
by Amar Shukla 17 May '20

17 May '20

External Email - Use Caution Hello Freesurfer, Can we go through the volumetric [surface area and many more ] through DTI images and T1 or t2 weighted images of the same subject. Can we provide common study and can we develop any analysis on these studies. My research is focused on these direction o or any kind of corelation through different Images . basis of diffusion images and T1 or t2 weighted images, so please give suggestions and comment on these. -- With Regards, Amar Shukla

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why fsaverage fold is a "link folder"
by ZhangBo 17 May '20

17 May '20

External Email - Use Caution Hi teams, For recon-all in parallel, why fsaverage fold is a "link folder"? I run recon-all in one computer (Ubuntu), and copy the result to another computer for analysis. And error happened when I need to use data in fsaverage folder. Thanks Bo

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 16 May '20

16 May '20

External Email - Use Caution 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

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Freesurfer May 2020