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
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng>
FsTutorial/GroupAnalysisDng - Free Surfer Wiki
<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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