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Hi Douglas,

Really appreciate your help and sorry for the confusion due to unclear questions.

1) Right, it was surface-based analysis. Below is the screenshot of the significant result (right volume) I got after running mris_preproc, mris_glmfit, and mris_glmfit-sim.

In the summary file, this region is right superior frontal. Could you please confirm that mri_segstats command you suggested will allow me to get the value presented in the figure above for each subject?

2) Sorry for the confusion. Would it be possible to show conventional p-values (0.05, 0.01, or 0.001) in the color scale instead of 1.75 or -1.75 in the image above?

Best,

JW

On Mon, Sep 6, 2021 at 1:18 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

On 9/3/2021 9:28 AM, Junyeon Won wrote:

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Dear Freesurfer experts,

Could I have a couple of questions regarding visualization?

1) I found significant clusters on the right hemisphere volume after glm_fit and cluster correction. I would like to extract the volume from this cluster for each participant. According to the freeview instruction (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization), the FSGD file (y.fsgd) should be loaded and select a point by clicking on the parametric map at that vertex to generate a plot for a particular vertex. I tried this but I am wondering if the mean value from the cluster can be extracted for each participant. I want to extract the values from each participant not just view the values through the FSGD file for further analysis.

You would not use freeview in this way. Is this a surface-based or volume-based anlaysis? If surface-based, do you mean you want to cortical volume of your significant area? If so, you can run preproc-sess with the same options you used for thickness, but --meas volume instead. You can then compute the volume for each subject with
mri_segstats --seg ocn.mgz --i lh.volume.mgz --excludeid 0 --avgwf table.dat
table.dat will be a number-of-subject by number-of-clusters table.

2) Could you please let me know if it is possible to show the p-value numbers on the color scale?

what p-value? can you be more specific?

Best,

JW

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