Did you download the patch? See the "
If You're Not at an Organized Course" part of this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
On 3/17/2020 11:31 AM, Varun Chandran wrote:
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 <mailto: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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