Thanks Doug. I will look those tools up! Regarding the spatial normalisation, would mri_cvs_register be suited for this purpose? Specifically, using the —mni option so that I still run the eventual comparisons in MNI space?
Best Wishes, Elijah On 9 June 2017 at 21:42:44, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote: On 06/09/2017 04:32 PM, Elijah Mak wrote: > Hi Doug, > > I am referring to a rather old thread where you have provided some > interesting suggestions to perform group-wise analysis of WMHs. I am > trying to do something similar in patients and controls. First, > mri_binarize was used to extract the individual WMH volumes from > aseg.mgz. These volumes were subsequently warped into MNI305 space and > smoothed (using mri_fwhm 8mm). The goal is to compare the spatial > distributions of WMH between both groups. Finally, mri_concat --mean > was used to visualise group averaged WMH volumes. The outputs can be > found here: http://imgur.com/a/curYf > > Do these steps look alright? On a conceptual level, is it > statistically valid to compare stacks of binarised lesion maps between > groups (using mri_glmfit and then performing MC with FDR/mri_glmfit-sim)? I'm sure there is a lot to find wrong with it, the data are not gaussian for starters. You might do better to use permutation with cluster or max correction (if your design is orthogonal, or use PALM). I don't have anything that will do voxel-wise permutation (which you would need to do an FDR correction), though you could do it fairly easily in matlab. > > On an individual level, I noticed that some WMH voxels show up inside > the MNI305 ventricles for a few subjects. This happens despite a > good-looking talairach registration. You are very optimistic about how good the affine registration is. If you were to look at the individual subjects, you would see that GM, WM, and CSF would be all over the place. Don't take the MNI305 anatomical image too seriously. Having said that, you can check the registration in the problematic subjects. > > Thanks a lot for your time in advance and I’ll appreciate any thoughts > you may have on this. > > Sincerely, > Elijah > > Dr. Elijah Mak, Research Associate > Department of Psychiatry, Old Age Psychiatry Group > University of Cambridge > Trinity College, CB21TQ, UK > http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
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