Hi Doug,
Many thanks for your help. I have one more questions please. You were telling
me that:
"Given that FA is very non-gaussian, a lot of people prefer to use
permutation". What this means? Do I need to run something different than:
mri_glmfit-sim \
--glmdir Group_Analysis.glmdir \
--grf 3 neg \
--cwpvalthresh .05 \
--overwrite
Thank you.
Antonella
________________________________
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, January 23, 2012 4:50 PM
Subject: Re: [Freesurfer] mri_glm with grf over CVS space
Antonella Kis wrote:
> Hi,
>
> I would like to do a Group Analysis for my FA data.
>
> For all my subjects (controls + patients) I have all the
> fa-masked.ANAT+CVS-to-avg35.mgz (the resampled registered image to CVS space).
>
> I am not sure if my steps for the Group Analysis are the right one:
These look correct
>
> 1) Concatenate FA from individuals into one file
>
> mri_concat */fa-masked.ANAT+CVS-to-avg35.mgz --o
>GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz
>
> 2) Make sure the order agrees with the fsgd:
>
> ls -l */fa-masked.ANAT+CVS-to-avg35.mgz
>
> 3) Create average of the input images for visualization:
> mri_average */fa-masked.ANAT+CVS-to-avg35.mgz
>GroupAnalysis.Average-fa-masked.ANAT+CVS-to-avg35.mgz
>
> 4) mri_glmfit --y GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz \
> --fsgd Group_Analysis.fsgd dods --C contrast.mtx --glmdir
>Group_Analysis.glmdir
>
> To view uncorrected results:
>
> tkmedit fsaverage orig.mgz -aparc+aseg -overlay
> /media/1Tra/Antonella_2011/DTI_FS/dtrecon/Group_Analysis.glmdir/contrast/sig.mgh
> -fminmax 2 3
>
> where -fminmax 2 3 : Voxel-wise threshold of 2 (p<.01), color saturation at 3
> (p<.001)
>
>
> To correct for multiple comparisons run:
>
>
> 5) mri_glmfit-sim \
> --glmdir Group_Analysis.glmdir \
> --grf 3 neg \
> --cwpvalthresh .0166 \
> --overwrite
>
>
> Is 3 (p<.001) neg as well as .0166 (.05/3) the best voxel-wise as well as
> cluster wise values to be tried?
There is no answer to the voxel-wise threshold (a criticism of the method). For
the CWP, you can use .05 instead of .0166 (that value is for the case where you
are doing separate surface and subcortical analyses). Given that FA is very
non-gaussian, a lot of people prefer to use permutation (which requires you to
run a simulation -- also see my note from last week about a bug in the
permutation code (not a problem if you only have one contrast))
>
>
> To view corrected results:
> tkmedit fsaverage orig.mgz \
> -ov
>/media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.cluster.mgh
> \
> -seg
>/media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.anat.mgh
> \
>
>/media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.lut
> \
> -fminmax 1.3 5
>
> with only positive values
>
> * p-values are p-values for cluster
> *
> Set threshold to 1.3 (p<.05)
>
>
> Are this steps right?
>
> When I run the registration over the cvs space which file is the equivalent
> file of the fa-tal.nii.reg from the TAL space?
I don't think there is one file that exists.
doug
>
>
> MANY THANKS!
>
> Antonella
>
>
>
>
> ------------------------------------------------------------------------
>
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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