It looks like you are using gender as a continuous variable. You should set up two classes, one for male one for female. You can then test for the AT slope with a contrast of
0 0 0 0 0.5 0.5
you don't need separate pos and neg contrasts

For mri_glmfit-sim, a threshold of 1.3 (p<.05) is way too liberal for the MCZ simulation. I would use permutation. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm

On 3/12/2020 6:30 AM, Varun Chandran wrote:

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Dear FS experts,

I am looking at the relationship between the cortical thickness and a behaviour measure, while controlling for the effects of age and gender. In this analysis, I am using CT_AT.fsgd, contrast_pos.txt and a contrast_neg.txt.

GroupDescriptorFile 1
Title Autistictraits
Class AT
Variables                         Age     Gender   AT

Input   Con_P001   AT   -4.142    -0.428    21
Input   Con_P002   AT   -8.142    -0.428    31

My separate two contrast files:

Contrast_pos.txt      0          0           0         1

                            

Contrast_neg.txt      0          0           0         -1

mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C Contrast91_pos.txt --surf fsaverage lh --cortex --glmdir glmdirlhposlat.glmdir

mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C Contrast91_neg.txt --surf fsaverage lh --cortex --glmdir glmdirlhneglat.glmdir

mri_glmfit-sim --glmdir glmdirlhposlat.glmdir --cache 1.3 pos --cwp 0.05

mri_glmfit-sim --glmdir glmdirlhneglat.glmdir --cache 1.3 neg --cwp 0.05

By changing the commands appropriately, I am looking at the right hemisphere too.

Can anyone please help me to clarify, if I am applying the command lines correctly? Any sort of help would be very much appreciated. Thanks !

best,

Varun Arunachalam Chandran

PhD scholar (Neurosciences)
School of Psychology and Clinical Language Sciences, 
University of Reading, Harry Pitt Building, 

Whiteknights campus, Reading-RG6 7BE,

Berkshire, United Kingdom.

                                        

 

                          

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