External Email - Use Caution Dear FS experts,
I am trying to run the cluster-wise correction by using permutation based
multiple comparison. For this, as you would know, we use: mri_glmfit-sim
In attempt to this, I tried running different options
mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_AT6.fsgd doss --C
Contrast91.txt --surf fsaverage lh --cortex --glmdir glmdirlh_lat3.glmdir
mri_glmfit-sim --glmdir glmdir${i}_lat3.glmdir --cache 1.3 pos --cwp 0.05
--3spaces
Since, there was recommendations in this forum to use --perm for 1.3, I did
so
mri_glmfit --y lh.thickness.AT.10B.mgh --X design_91subjs.txt --C
Contrast_CT91.txt --surf fsaverage lh --cortex --glmdir
glmdirlh_design.glmdir
mri_glmfit-sim --glmdir glmdir_design.glmdir --perm 1000 1.3 pos --cwp 0.05
--3spaces
However, it is displayed an error message 'design matrix is not
orthogonal', though I used CT91_AT.fsgd and not the design matrix --X
option.
Despite that, I tried again starting from design matrix with the
mri_glmfit, it was ok. For the same I used, --perm for the mri-glmfit-sim.
But, it was a same orthogonalisation error message.
I am also attaching my Group Desscriptor file: .fsgd, design matrix:
GLM_all_Scan_Mim_91subjs.txt and the contrast.txt files for your reference.
It would be great, if anyone could please help sort out this issue. Thanks !
kind regards,
Varun
On Fri, Mar 13, 2020 at 10:40 PM Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:
> 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:
>
> External Email - Use Caution
> 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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CT91_AT6.fsgd
Description: Binary data
0 0 0 1
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