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:
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?
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?
MANY THANKS!
Antonella_______________________________________________
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