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.*
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/MultipleComparisonsV6.0...
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./
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Doug,
Thank you very much for clarifying my doubt :)
kind regards, Varun
On Fri, Mar 13, 2020 at 10:40 PM Douglas N. Greve dgreve@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/MultipleComparisonsV6.0...
On 3/12/2020 6:30 AM, Varun Chandran wrote:
External Email - Use CautionDear 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.*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@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/MultipleComparisonsV6.0...
On 3/12/2020 6:30 AM, Varun Chandran wrote:
External Email - Use CautionDear 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.*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/MultipleComparisonsV6.0...
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 <dgreve@mgh.harvard.edu mailto:dgreve@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./ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Varun Chandran