Hi Jeff, after editing anything in the cross, you usually need to rerun the base (and then all longs). Also you need to edit the base (brainmask, talairach) as that is where the long processes take the information from. It is more important to fix the base than the cross in many cases.
More on longitudinal editing is here: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits Examples are in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial Good luck, Martin On Thu, 2011-09-01 at 10:24 -1000, Jeff Sadino wrote: > Hello, > > I finished processing my first longitudinal subjects, but I have some > errors. The TP3.long aseg.mgz file is poorly segmented (corpus > callosum, see attachment). I am wondering where I should make > edits to correct this. The surfaces of all 3 longitudinal timepoints > look fine, so according to the wiki, I should only have to edit the > TP3.long. Is that true? If not, then I will have to edit TP3.cross. > Originally, the watershed for TP3.cross was bad. I edited this and > re-ran autorecon2 and autorecon3, and exited with no errors. However, > the cross aseg.mgz is still bad. I thought maybe the talairach.m3z > file was bad, but the nu_noneck image was transformed fine. I see > that the log file says during the mri_ca_label step that the CSF peak > is too bright - rejecting (see attachment). After comparing the csf > areas of the TP3.cross norm image with the csf areas of the TP1.cross > norm image, they have values of 30 compared to values of 10. Previous > posts have suggested to copy the orig.mgz image to the nu.mgz image > for a similar problem. Can someone please advise me on where it would > be best to make the edits so that my longitudinal reconstructions are > accurate? > > > Thank you! > Jeff Sadino > _______________________________________________ > 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.
