The easiest thing is probably just to use matlab to load in the data (MRIread.m) and pull out the vertices you need. Alternatively, you can convert an mgh/mgz file to ascii  with mri_convert --ascii or --ascii+crsf and then do what you want with it.

On 3/21/2023 12:38 PM, Maria Czarnecka wrote:

External Email - Use Caution

Dear Sisters and Brothers in neuroscience

I am a huge fan but a very new user of the freesurfer, please treat me as such when answering this email.

I have successfully performed anatomical and functional data analysis using fmriprep, freesurfer and fsfast. I have all the files needed, everything looks perfect. As a next step of my analysis I would like to perform a correlation of Cortical thickness and the functional activation in one of my contrasts (I would like to correlate the CT with the z-scores). I would like to do that separately for each subject and in ROIs (ideally, self-defined Rois, but if there is an easy way to do it in anatomical ones I will be very happy as well). What I need is for the program to take the z-score from each vertex in an ROI and the value of cortical thickness for each vertex and do the correlation on those values. I can also do the statistics in another tool (R), so simply extracting those values for vertices in an ROIs would be great.

Do you have any suggestions how to do that?

Best,

Maria Czarnecka

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