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Freesurfer experts,

I have two questions that probably show my lack of understanding of many things related to thickness comparisons.

I have a group of controls and a single subject with pathology. I'd like to run a thickness analysis comparing them. I realize this is not ideal from a statistical standpoint, but due to the rarity of the disease, we'd like to see the results anyways.

Currently I'm using mri_glmfit followed by mri_fdr to do this comparison.

My questions are:

1) Is this FDR tool robust enough to handle this type of one-vs-many analysis? Is there a better way?

2) Generally, for one-vs-many analyses, I'd like to use a z-score. Is there a good way to convert this -log10(p) value from sig.mgh into a threshold for z.mgh instead? The dumb thing of back converting from p-value to z-score doesn't give the same maps once thresholded (there is probably an obvious reason for this that I'm missing).


thank you for any help you can provide!

quentin funk

Houston Methodist. Leading Medicine.

Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care and safety and one of the top 20 hospitals in the nation. In addition, we are nationally ranked in 11 specialties, the most in the state, and have been national leaders throughout the COVID-19 pandemic in research, offering innovative treatments and surpassing CDC safety standards. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine.


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