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 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.
