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.wags...@einsteinmed.org <mailto:mark.wags...@einsteinmed.org>_
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