Hi Venkatesh, try using mri_glmfit-sim and spec the permutation simulation method. This is just a front end script for what you have run, but it handles everything, including running mri_surfcluster to get the cluster pvalues. Another possibility is to run randomise on the output of mris_preproc? Just spec a nifti format as output. The cluster measures will not be valid, but the voxel-wise measures will be. doug

On 9/12/13 5:11 PM, Venkatesh Rajagopalan wrote:

Hi All,

I am trying to compare my VBM results from FSL with cortical thickness changes using freesurfer.

I would like to perform permutation based FWER correction to see cortical thickness changes. The reason to do FWER correction is I used randomise in FSL with FWER correction so I want to keep my statistical approach the same between FSL and Freesurfer to compare VBM and cortical thickness changes.

I extensiviely searched the archives but could not find an answer so posting this message

I ran the following command

mris_preproc --fsgd deisgn_all.fsgd --cache-in area.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.all_gps.area.10.mgh

mri_glmfit --y lh.all_gps.area.10.mgh --fsgd deisgn_all.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.all_gps.glmdir --sim perm 5000 1.3 csd1 --fwhm 7 --surf

I do not know how to run the mri_surfcluster command. I read few posts and tried running the following mri_surfcluster --src sig.mgh --csd csd-group.3.diff.csd --ocp sig_cluster.mgh

but I did not see any cortical thickness changes wheres I did see cortical thickness changes when simply using FDR option in the tksurfer.

Kindly let me know where I am making the mistake. Any help will be greatly appreciated.

Thanks Venkatesh

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