Hi Daniel. > i'm currently applying mri_cvs_register and I'm very happy with the nice > results. Congratulation for this very clever approach. However, some data > sets which I work on have still aseg.mgz which are not segmented > appropriately. As far as I understand aseg.mgz is not redefined after e.g. > pial-edits or added control points. Thus, I think it might be better to use > aparc+aseg or wmparc instead of aseg within mri_cvs_register. Taking this > into account I have the following questions: > > 1. Do you have experience with mri_cvs_register and --asegfname Option > different from aseg? Does it impact the processing time? Are there options, > which have to be adopted?
I only minimally experimented with this option, alowing users to use segmentation files that are edited or modified from the default version. processing time and registration options might change with a new file, but that will depend on thenature of the new file that you want to use. I belive that if you use either of the files that you mentioned above neither of those will (need to) change. > 2. Since I think it is better to use aseg instead of wmparc, since it > contains fewer IDs and registration will not be overfitted, is there a > convenient way to generate a new aseg.mgz, which includes manual corrections > like pial edits? If you make manual edits to the aseg.mgz file you can always save it under a different name and use the --asegfname option to indictae the new input to mri_cvs_register. For manual editing we recommend using Freeview and on the below page you may find useful advice http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSegmentations > 3. The last question regards the norm.mgz ... since it also often contains to > much (outer brain) volume .. would it be better to mask norm.mgz with (e.g.) > wmparc or a dilated version of wmparc before using it with mri_cvs_register ? That never caused a problem for me, and the answer in your case will depend on the amount of error that exists in your datasets. If you do decide to use a mask though, you should do that consistently on all of your data sets. Let me know if you have any further questions. Lilla _______________________________________________ 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.
