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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