On 8/19/2020 10:24 PM, Mark Wagshul wrote:
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Dear Freesurfer experts,
I have what seems like a simple problem, and I’m sure there is a method for doing this, hoping someone can give me some guidance.
We have results from an LME model run on surface data, and then run through PALM to calculate FWE-corrected p-values from the LME. We now would like to extract the mean beta values from each anatomical label region, within regions that were significant at p-corrected < 0.05. The beta values (as well as the PALM p-values) are contained in an mgz surface file.
So, what I think is needed is:
1) Create mask images for each individual label index, e.g. lh.caudalmiddlefrontal
You can do this in one of two ways: A. Use mri_annotation2label to create a "segmentation", then use mri_binarize with --match to pull out each label as a mask B. Use mri_annotation2label to break the annotation into separate labels, then use mri_label2label to create a binary mask
2) Create mask image from PALM results, for p < 0.05
Not sure about this, but you might be able to use mri_binarize with --max .05
3) Multiply mask * label * beta, and calculate mean value in that region
fscalc mask.mgz mul labelmask.mgz mul beta.mgz -o result.mgz
So, my simple question is what are the appropriate FS commands for performing this (or alternatively Matlab commands), or is there a simpler way or extracting these values?
Thanks for any advice you can give us on this.
Mark
Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email:_mark.wagshul@einsteinmed.org mailto:mark.wagshul@einsteinmed.org_
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