I think that contrast computes Female-Male regressing out Dx and age. If you
want HC vs MS, then use
-0.5 -0.5 0.5 0.5
On 12/29/2020 4:52 PM, Swanson,Clayton wrote:
External Email - Use Caution
Hi Freesurfer Team,
I am performing an analysis on 23 HC and 26 people with MS and I would like to
perform the stats appropriately. I would like to control for (or regress out)
age and sex. Therefore, I created my FSGD file which has 4 classes (HC_Male,
HC_Female, MS_Male, MS_Female) with age being the only variable. My contrast
for this analysis is: 0.5 -0.5 0.5 -0.5 0 0 0 0. Lastly, I want to run a
permutation analysis, so I set it up like this:
#!/bin/tcsh
setenv study $argv[1]
foreach meas (thickness volume)
foreach hemi (lh rh)
foreach smoothness (10)
foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
mri_glmfit-sim \
--glmdir {$dir} \
--perm 1000 1.3 pos \
--cwp 0.05 \
--2spaces \
--overwrite
end
end
end
end
After running the permutation, my next steps were to view the results in
Freeview with the command [ freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=perm.th13.pos.sig.cluster.mgh
] because it’s my understanding that would overlay the cluster-wise corrected
map and the view I get is an entirely yellow hemisphere. However, there are no
significant clusters when viewing the perm.th13.pos.sig.cluster.summary, so I
am a bit confused. Also, when I look at the uncorrected results with the
sig.mgh file there are a number of spots on the hemisphere.
Does this result mean that there are no cortical thickness differences between
HC and MS when controlling for Age and Sex? Or does this result mean something
different? What could be the next analysis steps I could perform?
My goals are to assess cortical thickness differences between HC and MS.
Thanks for any help you can provide,
Clayton
________________________________
Clayton Swanson MS
Graduate Research Assistant & PhD Candidate
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160
clayton.swan...@colostate.edu<mailto:clayton.swan...@colostate.edu>
(He/Him)
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