On 2/7/16 1:34 PM, Silas wrote:

Dear FS team,


I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng
surfer.nmr.mgh.harvard.edu
Introduction. This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including ...

1) I would like to do a surface based analysis where i'm only investigating a certain area or label - instead of doing a whole brain analysis. This can be done by introducing --label surface_area_of_interest.label when running mri_glmfit. Would this (in theory) give me different results from doing a whole brain analysis - or would it just exclude the results from outside the label?

No. However, if your activation is near the boundary of the ROI, then you may want to constrain the spatial smoothing to be within the ROI.

And how about after clusterwise correction for multiple comparisons?

If your new ROI is much smaller than whole hemisphere, then you will need to generate new correction tables (otherwise it won't help to constrain it to an ROI). To do this, see https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

-> is there a better way to do this than following the command-line group analysis stream in freesurfer?

No


2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when configuring the overlay?

This is the voxel-wise correction for multiple comparisons. The value of the voxel (and overlay config units) are -log10(p), where p is the p-value corrected for multiple comparisons. So p=.01 means 2.


Best, Silas



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