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Perfect, thanks so much for the quick response!
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.orgmailto:mark.wagshul@einsteinmed.org
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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Thursday, August 20, 2020 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting LME results from label regions
On 8/19/2020 10:24 PM, Mark Wagshul wrote:
External Email - Use Caution 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.orgmailto:mark.wagshul@einsteinmed.org
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