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 > > Kessler Foundation is proud to be recognized as one of the Best Places to > Work in New Jersey. > > The information in this transmission is intended for official use of the > Kessler Foundation. It is intended for the exclusive use of the persons or > entities to which it is addressed. If you are not an intended recipient or > the employee or agent responsible for delivering this transmission to an > intended recipient, be aware that any disclosure, dissemination, distribution > or copying of this communication, or the use of its contents, is strictly > prohibited. If you received this transmission in error, please notify the > sender by return e-mail and delete the material from any computer. > > _______________________________________________ > Freesurfer mailing list > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
